I've recently been through this and from advice from this forum (thanks) and Cake St. Classics (Richard?) the first thing I checked was the ignition timing. This is sound advice as if there is a differnce in timing you'll not sort out the root cause of the problem. In my case the drive side was running a fair bit hotter and I initially though of induction bias. However, having spent a little time and a bit of money on one of the SRM timing disc set ups I found that the drive side piston was firing 5 degrees retarded (having timed the ignition from the timing side). You should bear in mind that the mag had been refurbished and a new cam ring fitted. You could actually see the difference in the cam ring when you compared it to an original. Anyone want a cam ring with different ignition settings as I've got a brand new one in my scrap box? Anyway, once I'd thrown the new cam ring some distance up the garden and refitted an old one I found the timing spot on on both cylinders and now running well (even temperature). The use of a strobe, timing disc, and magneto timing buzzer all helps. I know that some people prefer to use fag paper and a stick down the plug hole, but it's nice to see the the bike running and the strobe showing you exactly at what degree it's firing on both cylinders.
Brian