So tell us, what ignition does it have ?
I'd also maybe suspect an air leak into the exhaust, maybe as things expand and get hot.
I'd have that side off, and carefully examine the seal in the exhaust port,
and where the muffler meets the exhaust pipe.
It doesn't take much of a hole to allow air in, and make some popping noises.
Other thing to try is to either tickle the problem side when its happening (watch the road), and see if :
- it can be tickled a lot, which may indicate a low fuel level in that carb, for whatever reason.
- if adding more fuel to that side makes the backfires go away, or makes it worse.
Failing that, a blocked idle jet could do this also.
Can you make it idle on just this cylinder, down to real low rpms. ?
Remember, it can take 3 or 4 cleans to get that idle jet system really clean...
I had an old engine with really worn valve guides, and new guides made something similar go away.
Something to think about, not knowing the history of your bike.
But this was accompanied by loads of blue smoke on startup, so was rather obvious....
Have fun !