What voltage have you got at the battery?A good battery is critical on these bikes.You need at least 12.5v at the terminals for reliable starting.Dont go by the voltmeter in the clocks either,...its not reliable.
The backfiring could be a leaking exhaust.My old 999 did that when the exhaust seals failed.It could also be down to unburnt fuel.
I'm thinking the latter.
Early 999/749's used to eat coils,...especially the front cylinder.Moisture from wet roads or a damp garage can creep in and cause corrosion.2005 onwards bikes had an improved version that is a straight swap.(The coils are built into the spark plug caps,btw.)
3.Check/clean plug caps.
Let us know how you get on.