Well, I finally scraped together the cash and bought a splitter, gaskets, seals, circlips and a crank puller. Got the cases split after breaking an arm off of a Tusk crank case splitter and welding the arm back on. Everything in the transmission looks brand new. I can see hardly any wear on the dogs, shafts, shift forks, gears or anything. The top end was also almost completely clean/free of carbon. The piston inside says ART on one side, anyone know what it is?
I pulled the gears off of the shafts, all of the circlips were in the proper location and looked good, so I put everything back together with the new clips. The 18 mm circlip on the end of the one shaft didn't really fit on too well, but looks ok. I have put the cases and transmission together without the crank about 5 or 6 times and played around with shifting it. It seems like it's a little sticky when I'm going through the gears, but if i'm spinning the output shaft by hand and I try shifting it, it goes through all of the gears. It almost seems normal, the same way any bike won't shift through gears when it's sitting still, but I'd rather be sure before I put it all back together. I'm going to pull it back apart and see if I can figure out a way to tell if the shift forks are bent, because at this point I think that may be the only thing that could be causing a problem.