So I've tried everything I can think of and the next step is taking it to a mechanic and getting bent over. Any ideas or input is appreciated. Here is the problem described as best and concisely as I can followed by a link to a video of the bike in it's current state.

2007 Ninja 250 3500 miles. Tipped over by my student while parking, wouldn't start back up after 15 minutes passed. As is typical during a tip over I felt it needed to sit before starting again as the carbs were most likely flooded. it wouldn't start so I parked it thinking it would self correct with time. Came back a week later, wouldn't start. There was gas in the CA emissions recapture filter. Drained that. Got it started. It will run but then idles off. I've removed the carburetor and "cleaned" it (mind you there are only 3500 miles on this bike and it was pretty clean to begin with), removed the petcock and adjusted the spring and spacer. Replaced the plugs, checked the spark. Ran the bike with the fuel cap open in case there was a problem with the breather valve in the cap. The bike will start every time however it will only run for a while and then die. I also removed the fuel filter in the line where it enters into the carburetor. After all of that it still has the same problem. I cannot tell if there is an issue with the fuel flow as it appears to be suffering from fuel starvation, or if it is something else. Today 1/11/14 I attached a cylinder of gas directly into the carburetor so as to eliminate any possible petcock issues. Problem remains. If I do not gas it, keeping the rpms up, it eventually idles to a halt. I've turned the idle adjustment valves 1,2,and 2.5 turns from fully in. Same problem each time. I sprayed WD40 on the intake manifold liberally while running to see it there was a vacuum leak. I noticed no change in the rpm. At this point I'm at a loss. I know very little about carburetors and have no idea what to attempt next. Any useful input is appreciated. Here's a link to the video.
http://i621.photobucket.com/albums/tt295/mymotorcyclepics/th_MAH04842_zps1b990261.jpg (http://i621.photobucket.com/albums/tt295/mymotorcyclepics/MAH04842_zps1b990261.mp4)

..........I know very little about carburetors and have no idea what to attempt next........

Welcome to our site, Sarge !!!

I see that your bike is naked.
Because of that, the connectors to the coil on the side of the fall may have been disconnected.

Another thing that happens after side falls is that one or both of the needle valves that control the level of fuel in the bowls get out of position and either keep the flow closed or leak badly.
Sometimes that can be solved by tapping on the body of the carbs with the handle of a screwdriver or something like that.

Now, you know very little and still you cleaned the carbs.
Did you check and adjust those valves and the level of the fuel in the bowls?
Would you describe how extensive and using what did you do the cleaning?

Is the level of your oil normal?

Stopping after a while suggests something is changing during the period that it is running.
One thing that could change is fuel level. If the engine uses fuel faster than can be replaced in the carb bowls, then fuel level will drop and bike will stall. When engine stalls, can you start it again straight away, or do you have to wait for a while before it will start again? If you have to wait a while then that could suggests a fuel restriction.
You have eliminated everything down to where the fuel line joins the carb. So lets look there. When you cleaned the carbs, did you remove the floats & needles & blow back through the needle seats to check if the passage from the seats to the fuel line was clear?

Very strange
You eliminated the petcock so my first guess is gone. If the engine revs OK and will idle below 2000 than the jets are good. I would double check float level and pilot jets otherwise.

I would look at the plugs. Maybe tighten up the gap. Could be a cracked coil. Weak spark. Could need carb balance. Or its just low on compression. What rpm will it hold and not die?

sounds like you've lost compression

It's pretty hard to kill and engine and lose compression in 3500 miles. I would look elsewhere. Ever if no maintenence was done it should still have decent compression. Another thing that is not related to the tip over, but could be part of the problem are the valves. They may be too tight. My bike with about 1200 miles on it, needed to be adjusted. They were all too tight.

What does the inside of the tank look like? Any rust?

When it stops running, open the float bowl drains and see if you get a steady flow of gas. I'm thinking you won't...

My advice is going to be a little unorthodox, but try following it. On your next fill-up, use Shell gas.

Ethanol in modern gasoline wreaks havoc, especially with carbs and is allow to get stale.

Go to your local auto supply shop and buy a few cans of Seafoam. (Why a few? Because you'll be using this stuff probably from now on after you see what it does.) Follow the directions listed on the bottle and pour a modestly small amount in your gas tank. See what happens. ;)

There is no "next fillup" at this point because the bike's not running. Down the road I will give that a shot but it won't help my issue at this very moment. To answer the other questions

No, there's no rust.

When engine stalls, can you start it again straight away, or do you have to wait for a while before it will start again? If you have to wait a while then that could suggests a fuel restriction.

I have to wait. Maybe 45 seconds to a minute

You have eliminated everything down to where the fuel line joins the carb. So lets look there. When you cleaned the carbs, did you remove the floats & needles & blow back through the needle seats to check if the passage from the seats to the fuel line was clear?

I did remove the floats and the needles and I sprayed carb cleaner in everything I could. Not sure if the passage was clear or not. I pulled the carbs out again today and will have another look in the morning.

...........I did remove the floats and the needles and I sprayed carb cleaner in everything I could. Not sure if the passage was clear or not. I pulled the carbs out again today and will have another look in the morning.

Carb cleaner can damage the two big flexible diaphragms that govern the needles.
If damaged and leaky, the carbs will not function properly because they become non-responsive to the vacuum produced by the engine.

Above, I asked about the level of the oil because fuel leaking from the carbs down into the oil and contaminating it and increasing the level seen in the visor.

Take a look at these for verifying level of fuel, which is also important:

http://www.ninjette.org/forums/showthread.php?t=140623

http://faq.ninja250.org/wiki/Draining_the_carbs

For total cleaning:
http://faq.ninja250.org/wiki/How_do_I_work_on_the_carbs%3F

http://forums.ninja250.org/uploads/222044.jpg

http://homepage.ntlworld.com/lemmingsdial/bike/fuel%20level.jpg

When engine stalls, can you start it again straight away, or do you have to wait for a while before it will start again? If you have to wait a while then that could suggests a fuel restriction.

I have to wait. Maybe 45 seconds to a minute

Open the drains immediately after it quits and see how much fuel flows out - that will tell you something.

Could you get your hands on known working carbs? That would eliminate that variable since you already have sorted out that it isn't the tank.

I took the diaphrams out before putting carb cleaner in there.

Open the drains immediately after it quits and see how much fuel flows out - that will tell you something.

I will try that next time. Good idea.

Could you get your hands on known working carbs? That would eliminate that variable since you already have sorted out that it isn't the tank.
Not without buying a set, no unfortunately.

I believe gas might have passed through the carbs into the oil, I haven't smelled it yet, will be doing that shortly. Would that cause the engine to idle to a stop? I would imagine it would just cause a poor environment for the engine but not cause the engine to idle to a stop (remember it hasn't been ridden in this condition yet).

My guess is the fuel tank vent hose is pinched and causing a vacuum in the tank as the gas drains. The rain goes under the seat between the tank - crotch area. Try running it with the fuel cap open.(no smoking please)

My guess is the fuel tank vent hose is pinched and causing a vacuum in the tank as the gas drains. The rain goes under the seat between the tank - crotch area. Try running it with the fuel cap open.

That would be an incorrect guess, as I stated in the OP the tank has been removed from the equation (opening the cap was one of the first things I tried). Thanks though.

Maybe I missed it somewhere, but I see you've done everything to the carb, but make no mention of the airbox or air filter. What condition are they in after the long tip over? On rare occasions oil can ran back into the airbox and air filter from the crankcase tube.

The tipover was just that. A tip over. The student was a smaller male and the bike was heavy for him. He was backing in to the curb and it started to go over. I thought he might recover. He didn't, it fell over go 0 miles an hour. I laughed at him, walked over and picked it up. That was the extent of it.

Opened up one side again today.
Here is a link to photos before cleaning a 2nd time. It looked very similar to this the first time.

Ninja 250 Carburetor Slideshow by mymotorcyclepics | Photobucket (http://s621.photobucket.com/user/mymotorcyclepics/slideshow/Ninja%20250%20Carburetor)
http://i621.photobucket.com/albums/tt295/mymotorcyclepics/Ninja%20250%20Carburetor/_MG_5901_zps908a2ca9.jpg (http://s621.photobucket.com/user/mymotorcyclepics/media/Ninja%20250%20Carburetor/_MG_5901_zps908a2ca9.jpg.html)

You mentioned that you drained the CA emissions recapture filter. However on the parts diagram there appears to be two separate canisters. Could there still be fuel in the second canister interfering with proper carb function?

I emptied both. They are both closed but I opened the lines and drained what was there. The square one had no gas.

Those carbies look perfect. This is a strange one.

Sometimes when I've had a bike with a running problem, and the carbs have been triple checked, I later found a blocked breather pipe to be the problem. Maybe try temporarily disconnecting all the breather pipes from the carb (not vacuum ones) to see if this makes any difference. Remove the vacuum one from fuel tap and plug it & use your fuel bottle setup.

It's hard to see how a tip over could block a breather, but strange things do happen.

Also you could do a fuel flow test. With your fuel bottle hooked up, remove the fuel bowl drain screws and let it drain for a while to see if there is any change in the flow rate, indicating a restriction to flow.

Also in the video you had it running at 3000rpm to begin with before it slowed down & stalled. Can you adjust the idle speed back to idle at 1500rpm at all upon starting? Can you rev the engine, or does it rev normally upon starting? Does turning the choke on extend its running time?

Are the holes open in photo #26? How did you clean the actual jet opening?

this is interesting, i would first think Idle issue(adjust idle screw) and then bad gas, good luck.

So I went through the other side and cleaned that as best I could (again, it doesn't seem to have that much gunk/buildup but this is the first set of carbs I've opened up).Blew air through every line and they all seem clear. Reassembled. I measured the floats. One was significantly out of it's tolerances. 17mm +/-2mm was the number I found should be the height for the floats. One was at 18mm and the other was at 15mm. I adjusted the 2nd and they are now within 1mm which you can visually see in the link to the video below. Also they do not move in unison now (I believe they did before) which you can also see in the video. I don't know if that's a problem but I'm betting it very well may be. Input from those knowledgeable would be appreciated at this point.
http://i621.photobucket.com/albums/tt295/mymotorcyclepics/Ninja%20250%20Carburetor/_MG_5964_zps50706ed5.jpg (http://s621.photobucket.com/user/mymotorcyclepics/media/Ninja%20250%20Carburetor/_MG_5964_zps50706ed5.jpg.html)
http://i621.photobucket.com/albums/tt295/mymotorcyclepics/Ninja%20250%20Carburetor/_MG_5974_zps013c4db9.jpg (http://s621.photobucket.com/user/mymotorcyclepics/media/Ninja%20250%20Carburetor/_MG_5974_zps013c4db9.jpg.html)
Video
http://i621.photobucket.com/albums/tt295/mymotorcyclepics/Ninja%20250%20Carburetor/th_MAH04844_zps12e9dbb1.jpg (http://i621.photobucket.com/albums/tt295/mymotorcyclepics/Ninja%20250%20Carburetor/MAH04844_zps12e9dbb1.mp4)

Also you could do a fuel flow test. With your fuel bottle hooked up, remove the fuel bowl drain screws and let it drain for a while to see if there is any change in the flow rate, indicating a restriction to flow.
Good idea. Will try.

Also in the video you had it running at 3000rpm to begin with before it slowed down & stalled. Can you adjust the idle speed back to idle at 1500rpm at all upon starting? Can you rev the engine, or does it rev normally upon starting? Does turning the choke on extend its running time?
That's the idle speed at startup. Adjusting the idle screw causes the rpm to vary greatly. Even when opening it the same thing occurs, so I tried to keep it right at closed or barely cracked. And if I coax it I can get it run longer but eventually the same thing happens.

Are the holes open in photo #26? How did you clean the actual jet opening?
All the holes are open and I went thought every one with a couple of twisted together strands of copper wire.

this is interesting, i would first think Idle issue(adjust idle screw) and then bad gas, good luck.
You know I hadn't even thought to adjust the idle screw, I went straight to pulling the carburetors out. Silly me.

In the interest of keeping the thread on point and not unnecessairly long for those people who might refer to it in the future, please try not to comment for the sake of commenting . Thanks.

That's the idle speed at startup.

3000rpm is kind of high for idle, unless the choke was on. Has it always been that high, or only since the tip over?

Adjusting the idle screw causes the rpm to vary greatly.
Do you mean that small adjustments cause it to either idle high or stall, with no middle ground?

Even when opening it the same thing occurs, so I tried to keep it right at closed or barely cracked.

I assume you are talking about the choke here? So choke does not help?

In the video showing the float operation, you had the carbs positioned so that the float pivot pin was at the bottom. Usually the best way to check is with the float pivot pin at the top so the floats are hanging. Then gradually tilt carbs back until the float tang just rests on the needle. If you tilt it any further then the weight of the floats will compress the little spring in the needle giving you a false float height reading.

3000rpm is kind of high for idle, unless the choke was on. Has it always been that high, or only since the tip over?

Since tip over. Choke off. Engine not quite warm


Do you mean that small adjustments cause it to either idle high or stall, with no middle ground?

Yes

I assume you are talking about the choke here? So choke does not help?
Choke does not help
Then gradually tilt carbs back until the float tang just rests on the needle. If you tilt it any further then the weight of the floats will compress the little spring in the needle giving you a false float height reading. I did it that way when measuring just grabbed it wrong for the video.

Ok. I've seen these symptoms before on older models with high mileage, and it's usually worn carb slides & butterflys leading to lean mixtures, or leaking inlet valves. But with your bike having so low mileage, it's still pointing to a fuel restriction, or an air leak, or perhaps the balance screw between carbs being way out.

You said you already tried the idle mixture screws at a few different number of turns out, up to 2.5 turns out. For an experiment, perhaps try turning them out to four or five turns, to see if this improves the idle speed fluctuations.

I have the idle mixture screws out 2.5 rotations (I set these while on the bench so there's no mistake as it was hard to do while on the bike. One 360 degree rotation counting as 1). I do not know how to check for air leaks. Can you tell me the best way you know of? The vacuum part of this thing is still conceptual to me and I'm very cloudy about how it actually works.

btw, I don't think it's the balance screw because I can't see any way of that having gotten changed simply because of where it's located and the fact that it was running fine before. Also there's a big yellow alignment stripe that I believe was put there for a reason.

Turn the idle adjustment, counterclockwise a quarter to half a turn to lower the idle down and set it to full choke. Start the bike and what RPM is the idle?

Find a nice big empty parking lot or a long empty street (preferably close to home) and give her a good ringing.

This is odd and it all points to fuel starvation. The only thing I can possibly think of is your float needles are getting stuck closed. Or a fuel/air passage is partially clogged. When the engine starts to bog and die, give some good solid taps on the float bowls and see if it keeps the motor running. If it does, than your needles are sticking for some reason.

I have the idle mixture screws out 2.5 rotations (I set these while on the bench so there's no mistake as it was hard to do while on the bike. One 360 degree rotation counting as 1).
Yes 2.5 turns is a normal amount, but to adjust while on the bike you can make up some little screw drivers like I have pictured, out of an old spoke or piece of wire, just using a hammer & file to shape the flat blade to suit the screw head. This adjusting out to 5 turns is just for diagnostic purposes, to see what, if anything, happens.

I do not know how to check for air leaks. Can you tell me the best way you know of?
You have already done some basic checking with spraying WD around the manifold. Another check is to disconnect the vacuum pipe from the fuel tap and plugging the end to eliminate an air leak from the fuel tap diaphragm. Another method is clamping each one of the pipes with pointy nose pliers, one at a time with the engine running, listening to see if the problem goes away or the engine runs better when a particular pipe is clamped.

The vacuum part of this thing is still conceptual to me and I'm very cloudy about how it actually works
I don't fully understand how it works either. A far as I can tell, the little chamber on the LH carb only works when the throttle is closed from high RPM. Vacuum acts on a diaphragm pulling a plunger open which alters fuel mixture, kind of like how the choke plunger works.

btw, I don't think it's the balance screw because I can't see any way of that having gotten changed simply because of where it's located and the fact that it was running fine before. Also there's a big yellow alignment stripe that I believe was put there for a reason.
I do not think it was your initial problem, or that it was altered by the tip over. I only mentioned it thinking that you may have tried adjusting it to cure your problem, only to create another one.

..........I do not think it was your initial problem, or that it was altered by the tip over. I only mentioned it thinking that you may have tried adjusting it to cure your problem, only to create another one.

I fully agree.

Normally the problem we have has been originated by the last change we did or the last event: the tip over in this case.
The more unrelated things we change (based on mere assumptions), the farther from the pre-event conditions we move.

Ever checked coils' connections (in and out)?
Level of fuel in each bowl?
Gasoline in oil?

Another possible test to verify that the valves are not sticky, as suggested by cuong-nutz above:

Connect a transparent hose to the carbs inlet, fill it with gasoline and open the drain of each carb alternatively.
If the column remains for one or both bowls, that valve is not opening, even when the level in that bowls drops.

So this is what I did. Opened the other side and cleaned that also. Used copper wire and stuck it in every hole there is, clear or not (they all looked pretty clear however as can see in the photos). Compressed air and carb cleaner. Adjusted the float height of one, which as I said before, was off significantly as compared to the other. Lithium grease on one of the diaphragms that looked dry. Idle adjustment needles screwed out 2.5 turns. Reassembled.

Kept my I.V. gas setup in place to test. It runs. Drove it around for 10 minutes checked everything and put it away for the night. Came back today and ran it for about 10 minutes to verify it was still running. It was so I replaced the tank and reassembled most things that needed to be removed to get the carbs out. Ran it again. Put it away

Now here are 2 things I did that I didn't do the first time. I dropped the oil and replaced. As I suspected from reading about similar problems, the oil smelled like gas. That indicated the petcock was leaking and gas passed through the valves and mixed with the oil. Was that the cause of all the problems? I don't know but I'm thinking so. The fall was to the opposite side of the petcock but maybe it was failing already, don't know. There was remnants of gas in the airbox also. Now I know gas didn't get everywhere from the simple tip over, but from the resulting cranking of the starter and all the other attempted "remedies" gas somehow got into the emissions canister, airbox and oil. Now like I said before I'm not a mechanic and this is all new to me so that's just speculation. It's running now, and idles right. Hopefully it will continue to do so. I have a lesson tomorrow. Assuming the oil stil is not fouled I will replace it again along with a new filter since the one in there now was also saturated with gas. Thank you to everyone that contributed their insight and help.

So this is what I did. Opened the other side and cleaned that also. Used copper wire and stuck it in every hole there is, clear or not (they all looked pretty clear however as can see in the photos). Compressed air and carb cleaner. Adjusted the float height of one, which as I said before, was off significantly as compared to the other. Lithium grease on one of the diaphragms that looked dry. Idle adjustment needles screwed out 2.5 turns. Reassembled.

Kept my I.V. gas setup in place to test. It runs. Drove it around for 10 minutes checked everything and put it away for the night. Came back today and ran it for about 10 minutes to verify it was still running. It was so I replaced the tank and reassembled most things that needed to be removed to get the carbs out. Ran it again. Put it away

Now here are 2 things I did that I didn't do the first time. I dropped the oil and replaced. As I suspected from reading about similar problems, the oil smelled like gas. That indicated the petcock was leaking and gas passed through the valves and mixed with the oil. Was that the cause of all the problems? I don't know but I'm thinking so. The fall was to the opposite side of the petcock but maybe it was failing already, don't know. There was remnants of gas in the airbox also. Now I know gas didn't get everywhere from the simple tip over, but from the resulting cranking of the starter and all the other attempted "remedies" gas somehow got into the emissions canister, airbox and oil. Now like I said before I'm not a mechanic and this is all new to me so that's just speculation. It's running now, and idles right. Hopefully it will continue to do so. I have a lesson tomorrow. Assuming the oil stil is not fouled I will replace it again along with a new filter since the one in there now was also saturated with gas. Thank you to everyone that contributed their insight and help.

So everything is working well? :thumbup:

I just recently have been having a similar problem and will try to clean my carburetor.

Hi,
I'm new to the group. I just bought a 2003 ninja 250, and I'm rebuilding the carbs because one is leaking from the overflow, and it's been sitting for a while, and float is stuck or trash in the needle seat. I noticed in the picture above a clear hose running out of the center of the carb, and noticed after pulling mine, that It didn't have this hose. Where does that connect to? It has the nipple for the hose to connect, but nothing is connected to it. thanks!! Looking forward to getting, and sharing ideas, and stuff on here. :dancecool:

Nevermind, Apparently it's an overflow line, that the dumbass mechanic that checked out the bike before I bought it, and supposedly fixed the carburetors(but didn't) left off when he worked his magic...ugh:clapping:

Welcome, Steven !!! :grouphug:

Yes, that is an overflow hose that dumps onto the road, just in front of the center-stand.

The soft components of the carbs become harder with time and should be replaced with fresh ones.

ducatiman may be able to help you with a repair kit at good price that he sales.

Welcome to the group!