Cooler heads prevailed (drank a couple of beers), and I pulled off the clutch cover and found my problems. Somehow (probably when I took the cylinder off to rebuilt the top end) the rod came out of the little plastic retainer and the lobed gear thing was stuck. Cleaned everything up and made sure everything was moving properly, replaced one of the plastic retainers (local cycle shop has some parts for LTs and TRXs--very handy) and the gasket, put everything back together and everything seems good.
Not even remotely as complicated as I was dreading it was going to be. These things are cake to work on!