Hey guys, it's in.
I took everything apart to make sure the clutch disc would actually go on the transmission splines (I didn't check it originally). It was tight, but A-OK. I also changed my rigging to get rid of the ratchet straps and just go with the floor jack cup on the transmission mount bolts in the back and the front of the transmission on the studs in the middle bellhousing holes. That let me start with the jack way low and give it one pump each time I fiddled. Eventually it went together, so it was just the angle of the dangle. With a lot of wiggling I got all the bellhousing bolts in by hand. I had to raise the back of the transmission way up to help ease in the top bolts. The very last quarter inch was on the dowels which had to be pulled together. Maybe I dinged them with the studs in those middle holes, I dunno. They seem OK.
The shop manual says to connect the master before stabbing. I think to keep from opening the bleeder on the slave and letting air in but the slave really doesn't want to move like that. This time I didn't connect the master and left the slave bleeder open the whole time to let the slave compress, and of course at the end my clutch pedal was garbage.
I tried to vacuum bleed the slave with the master connected and got a lot of air out. Ironically that made the pedal worse! So I took off the master and bench bled it again stringing out the lines and tapping. It was very tough getting the quick connect back in, I think because the slave was completely bled from the vacuum bleed. But it did snap in with force. Maybe this was why I couldn't connect the new slave originally as it was prebled.
Anyway, with the well bled slave and the bench bled master my pedal is pretty good getting travel on the slave right away. So I am hopeful the rest of the project will be uneventful now.
Thanks everyone! I was really doubting myself on every step after the pilot bearing issue. It was good to get some assurances on things.