i'd resolve to ditch this "custom" PO mod.so the bike has a big hole in the front of the muffler so has more roar sound (previous owner did that)
things to check:
1- battery terminals and cable ends pristine and tight?
2-sounds like alot of starting and starting and revving and idling on your part. plugs fouled? the NGK iridium tips will foul contrary to popular opinion.
3. is the IAT switch connected? in all likelihood you would have disconnected it when removing air box base during plug install. check the wiring plug.
4. all these multiple tps resets you speak of totally unnecessary. did you perform it correctly and then take a gentle ride in "learn mode" for the system to adjust?
5. how old is this fuel you speak of?
6. though your battery came back to life as you mentioned they are never ever the same after being completely drained to infinity. fully charge it and have it load tested.
report back with results.