I'm having the same problem as Special Man. It is NOT in the carbs. Here's my story:
I rebuilt the carbs, set the valves, sync'd the carbs, everything was nice. It started easy, ran good. Let it sit for awhile since I had accomplished what I set out to do. When I next try to start it, no joy. Nothing works. I get it running with brake cleaner and notice the right pipe is cold. Pull the plug wire, it's still loping along, nothing changes. Here's the goofy part: if I pull the wire off and hold it way off the plug, to where the spark is arcing to the plug, the cylinder fires and the bike runs great! I figured this was a bad wire, so I swapped in an extra wire I had. No change. After I caught onto the pulling the boot halfway off making it fire thing, I swapped the plugs side to side, and sure enough it moved to the left cylinder. Two new NGK plugs later and after a short period of running well it's back in the right cylinder. I'm stumped.