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.I have an 08 700 with dmc duals, cp11:1, hc3 and a msd. The bike will start fairly good with a decent plug in it but shuts off within a few seconds. I have adjusted the tps and played with the tune. If I give it gas I can keep it running longer but it cuts out and pops and help appreciated.
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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.