Ok, the transmission is set. It took a few tries, but I had photos of the engine from before I took it apart, and that helped me get the shifter in the right spot. I was able to go though all the gears. It was hard to move the shifter by hand, but I'm sure once there's oil in there it will move smoothly. The cases are all clean and ready to go back together. I just need to replace a few oil seals.
I'll search the boards for opinions, but what grease is generally used when reassembling? Cam shafts, main bearings, Etc. all need something. Shop manual just says "lubricate" but not sure what's best.