[Chasekito]

Hello everyone, first post but been reading forums for a couple weeks now. Got my first bike a couple weeks ago but have rode my buddies bikes here and there.
Little background - my buddy who loves flipping anything and everything calls me one day saying he bought a 08 ninja 250 that wasn’t running but had a friend with him who swore he could get the bike going. They couldn’t figure it out and he was frustrated it and knowing I have always wanted a bike asked if I would like to buy it. Being a little mechanically inclines I stopped by and before I get out of the car I see the first problem. His “friend” who weighed about a buck 20 and looked like he had been up for a month was bouncing around. I get out and very kindly tell him to stay away from it. The bike had no electrical power, had been wrecked and looked like 6 tweakers had there way with it. Feeling bad for my friend and me knowing about electrical I decided to buy it off of him feeling I could get the bike at least somewhat ridable. I also always wanted a street bike and it only having 9k miles on it I took a chance.
I first looked at the fuses. The 30 amp fuse was blown. Replaced it and now have power. (This is going to be easier than I thought) tried to start the bike and blew the 10 amp ignition fuse. A lot of the wiring was taped with electrical so I started following the wiring and found ground wires cut and not going to anything. I then grounded them, Replaced fuse and blew it again. Cut off all electrical tape exposing all wiring and seen the green wire going to right side ignition coil. It also had a pigtail ground wire going to the frame. Took it off and replaced fuse. The fuse didn’t blow and the engine turned over but no spark. Replaced ignition coils, spark plugs, plug wires, cleaned carburetors, replaced old gas. Tried starting the bike and as soon as I released the starter button it fired up. Thought that was weird but it was now idling. Drove it up the block and back. No problems at all. Quick response to throttle and nice power ( never driving a 250 and only ever ridden 600s it was slow for me topping out around 90 mph. But I finally had a street bike. Put around 100 miles on it. One morning I woke up drove it up my hill from my house and went about 1 mile. The tachometer started jumping and it felt like it wasn’t getting gas. Turned around putted up hill only going 30 mph. Since that’s all it would go. If I gave it too much throttle it would bog down and only stayed “running” at a certain throttle position. Pulled into driveway and noticed the exhaust was so hot it was glowing bright red on inside and after cooling down left my ever so clean looking exhaust halfway black. Took out spark plugs and tested. No spark on right side and only spark on left after releasing starter button. I can pop start it no problem but still only firing in one cylinder. The other cylinder keeps sparking after the bike starts running. Have 12v to ignition coil wire and even tested after that to the boot and even spark plug. I switched coils and plugs to other sides of each other and still the same problem with the right side.
The kickstand safety switch (just found this out last night) is missing something or something is wrong because I tried to start the bike in first on accident and it lunged toward. Kickstand down.
Don’t know if that has anything to do with coils but want to get everything out there.
Any suggestions are very appreciated and will with answers progress.
Thank you