I took the bike to a buddies house today. He knows these things pretty well, come to find out a mouse must have made a nest in the right side pipe which was clogging it up and choking it out. We got it cleaned out pretty well, and its a lot faster when both cylinders are firing properly.
I want to thank everyone for their input, this thing has been driving me crazy since I started working on it again.
I had blown out that pipe before, but my air gun wasn't as good as his. As soon as he started blowing air through it, chunks of oily grass started shooting out, and then all of the sudden, the big nest blew out. The left side exhaust still seems to blow a little harder at the muffler, but I'm gonna run it for a while and see what happens.
Thanks again,
Grason