Good work so far, but you haven't completed the tuneup yet. Before playing with the carbs, you still have the timing to do, the Cam chain tension to adjust, the air filter to clean/replace, the spark plugs to clean, gap, verify correct numbers.
Then you can check pilot screw settings, carb sync.
Then you check head pipe temps at idle for even temps. A cold one may be blocked slow jet.
If you have changes to exhaust sytem or intake from stock, you may have some carb jetting/tuning to do.
If you still have backfire issues at this point, check for induction leaks or leaks in the exhaust system.
If you run out of ideas, give us an update and ask more questions.
Cheers,