A useful tool for measuring the round of your piston big end caps and the engine cylinders (in conjunction with a digital caliper) is the telescoping gauges. They're spring loaded and they shoot out while theyre inside your cylinder and you tighten the knob to lock the measurement in place and then measure.
http://www.harborfreight.com/6-piece...-set-5649.html
The valve spring compressor is pretty much a must in my opinion if you plan on taking your valves out. I wasn't able to find any generic model that would actually work with the 250's head. I bought mine off ebay and it worked great.
http://www.ebay.com/itm/Heavy-Duty-5...item1c2c383c5f
You'll need a full set of metric sockets, I'd recommend both deep and standard length. Oil pan, shop rags, beer, music, electric drill with a screw extractor set and hammer, engine stand or small dolly, I'll try to think of more than that.
I'm in the process of putting a steering damper on (even though I think my new front tire alleviated my issue). You could try that out. A jet kit and new rear + front shock is pretty much a must in my book. It'll give you a whole new bike. The bore out is gonna be awesome as well even though I've never done it.
Stainless Steel brake lines up front at least would be a pretty good upgrade. You could play around with a bigger master cylinder if you wanna get crazy.
Maybe a +1/-4 sprocket setup.
Sintered brake pads up front.
I'd say a digital/analog gauge combo but I don't think you have a streetfighter. The fairings and windscreen help this bike a lot fyi....
Bigger tires.
Gear shift indicator.
I think I might throw a fuel pump in the tank one of these days. The bike seems to perform better with a fuel tank and I think it may be the extra bit of weight up top......
For the clutch assembly you're gonna need a clutch holder tool so you might wanna save up/buy that now.