The good news is that the idle is buttery smooth, and the rattle is gone, so I guess it's a start.
EDIT: I'm an idiot. I took the clutch off to take a peak and as I expected, the shift shaft arm was not over the little pin, but beside it. It must have wiggled it's way loose when I had the side cover off. Time to drain the fluids and pull the cover off again. This sure has been a learning experience for me, and on the brighter side of things I'm getting really good at changing oil, coolant, clutch plates, and pulling that side cover off.
Edited by nnamssorxela, October 07, 2012 - 02:47 PM.