[tooseevee]

This is not a fake account and you can believe in this problem.
I generally ride at RPM between 2000 and 3500.
The bike runs smoothly when the engine is not heated.
The real problem starts when engine gets hot.

     I agree with a few others here. I don't think it's heat-related. I think it's rider-related. I think you're lugging the engine. But I think too much so wadooweyeknow? 

[SteveThackery]

     I agree with a few others here. I don't think it's heat-related. I think it's rider-related. I think you're lugging the engine. But I think too much so wadooweyeknow? 

I agree - 2000rpm is too low and putting any load on could easily cause drivetrain shunt.  But how do you explain the MIL?  That's what's bothering me.

[NJ Mike]

I agree - 2000rpm is too low and putting any load on could easily cause drivetrain shunt.  But how do you explain the MIL?  That's what's bothering me.

If it's about to stall, or if it's too hot to even run properly, anything is possible.

[Breezin]

Or it has stalled,  and has restarted with the bike's momentum. Which would fit with extreme lugging.