Exup valve all free & adjusted correctly with a bit of cable free play?
Check actuator's not seized, crank motor over with kill switch "Off" while watching Exup pulley, pulley should rotate clockwise about am 1/8th of a turn & return back rest position after cranking.
Back-firing on over-run? I've had this issue with my Kawy ZRX11 ... tiny O-ring missing from carb mixture screw (previous owner) I might add, backfired like a bastid till I found it when I pulled carbs to apart.
Have u pulled main loom multi-plugs apart to check for bad connection & corrosion? especially plugs in left side fairing.
I assume you've a good battery? & checked all resistance limits on ignition & charging system, all can make bike run shite.
Have u fitted Iridium plugs? older ignition systems tend not to like em, probly best to stick to original spec plugs.
What type of air filter fitted? K&N's make any bike run like a bitch if even slightly over oiled.
Let us know how you're getting on, all being well the fault will be found?