My 98 warrior had the same problem. It terned out to be the parking brake. Try disconnecting the parking brake wires. Thats what I did to mine and she runs like it did when it was new. It is a BAD SENICE
I Have A 2000 Yamaha Warrior And The Problem Is It Keeps Backfiring And 'Missing'. What Could Be The Problem?
Your reverse shifter isn't disengaging all the way
Timing is off. This could mean that a belt has slipped or something but for some reason, the backfire means it is firing when the valve is open and missing means it does not have fuel when it should.