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.