Motorcycle Repair: r1 problem, yamaha r1, pulse generator

Question
i have a 2001 yamaha R1. when i run it for a while it breaks up bad. its running at normal temp.when it cools back down it runs fine again till it gets hot again.i changed the main jets thinking it was way to lean (and it was) and havent run it much since. just curious as to what it could be. thanks

Answer
Steve,
have you tried reading a new set of spark plugs,
if so, do they look black=rich or light colored=lean fuel.
Have you checked the air filters and choke etc.
It is hard to tell without being there,
but does it break up like it's running too rich on fuel/air?
Possibly it runs ok cold and then is too rich once warmed up.
Do you have the factory exhaust system?
If so have you checked the exhaust servo unit?
Maybe it is restricting the exhaust when hot.
Lastly, I suppose a pickup or pulse generator
could be acting up as it warms up.
Unfortunately even the factory is reluctant
to give specs for testing some electronic components
like ignitor units, (under the seat)
Make sure all your electronic connectors look okay.
Run it during the break up phase, stop the engine
quickly and see if the plugs tell anything about what's
happening in the engine.