OK, one last issue. I apparently lost overdrive somewhere in this affair. I can be going 65 in third(~3500 rpm), let up on the thottle, and no upshift. Normally I'm at 2500 at 60mph, so I know it's not upshifting. I tried cycling the OD switch on the shifter and had no luck. The light doesn't come on except when the switch is. I'm guessing I screwed up or forgot a wire somewhere. CEL is not on(yet). Any ideas on where to check first?

Only about 15 miles on it since I got it running, and it's a bit rough yet- I imagine that the 15 miles I put on it with two cylinders out would have made those two a little bit crusty and would explain the slight roughness.

Bourge, sending you a PM now.