Just fix a similar problem to yours. Bike would start fine (most of the time) then as it warmed up it would start to miss fire and cough. Then for no particular reason the bike would then run fine. When it had starting problems it would start with a cloud of black smoke (engine flooded I guess)
The problem in my case was a buggered/green/fury TPS and temp sensor. The temp sensor was sending error messages and the TPS would go from closed to full open with the smallest movement of the throttle.
Have a look/test your TPS and temp sensor. IMO I would think if the ECU was stuffed the bike wouldn't run
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