Have you tried unplugging the MSD? Could be TPS is miles out, could be dodgy wiring. Yamaha electrics were never the best in early 2000s to start with. The fact it's going with a pop sounds like it's over fueling and flooding out. Could even be a dodgy spark plug or coil on its way out.
Start with the free stuff. Remove MSD and see if that works. Check for any signs of damage to wiring or wires being pulled or plugs not quite seated right. Check TPS, there is away to check and set back to factory, but for the life of me I can't remember how.
Then move to cheap stuff, replace spark plug, if still no different, replace coil. Hopefully you don't get this far down the list and the problem is solved.