Ran the bike through the gears pretty hard today, and when I backed off it started running on one cylinder. When you open the throttle more, it starts running on two again with an occasional backfire through the exhaust. Changed plugs and no change. Anyone have any ideas what the problem may be?

Blocked idle jet?

do check the voltage at the coils and CDI units and the wiring mod in the FAQs.

I was thinking of the coils also. Be sure to check corrosion on the pins where its connected to the wiring loom. Had a simular issue couple of years ago. Some sandpaper on the connection pins and it was running on both cylinders again.
Léon

Thank you, I'll start with the coils then to the carb. Sorry for the late reply, haven't been online for awhile.

I agree with the plugged jets theory.
Phil