I feel your pain bro...didn't get shit for riding in, did get about an hour in late friday night, but I think my top-end may have went bye-bye; haven't gotten a chance to tear into it yet to find out. Cleaned my carbs & they were fine, didn't really do much more since I had the buggy there and haven't gotten to drive it much lately. Mines' doing similar to what you're describing, but I have no exhaust on the left side, dunno if there's spark or not, could be the coil...dunno yet. Owell, if it's the top end it's time for a better port job & new pistons, the stock 97's gotta be getting tired anyway.
You may try swapping the stator, knowing that you got on it & kicked the shit out of it and suddenly had spark...makes me want to say there's a lose connection somewhere. GD I hate troublshooting electrical issues.