A bike with electronic ignition will not want to start or run right if the battery is a little weak. The motor may seem to crank over fine, but the starter saps the energy to the ignition, so it won't start (or runs badly).
Loose or corroded battery connections can also cause the same symptoms.
An intake leak and/or faulty timing can also cause uneven running and backfiring.
Uneven exhaust pressure can indicate a valve (or piston) problem. Do you have any way to check the compression in each cylinder? Do it with a warmed-up engine and with the throttle & choke wide open, BTW.
Just some random thoughts I'm throwing into the mix.
If it ain't broke, don't fix it.