Couple of things to check out: is it possibly running to hot?, Does the pee stream look ok when running?, is the fuel tank venting correctly?, ignition coils can act up after getting warm, do you have fire in both cylinders after warm up?.
i had this problem after overheating accident.
head gets warped and compresion goes down, maybe water can intrusion into cylinder
and bad powerpack after overheating(electronic components can go down when warms up)
