OK, finally had time to work on this again.
I swapped some of the internals and the bellhousing/pump asy from the replacement trans over to my truck's original case. I rebuilt the replacement VB using the Superior kit and swapped that in too. Everything is torqued to specs and the bands are adjusted to specs. The harness is plugged in and there aren't any loose connectors hanging around. The new aux trans filter is installed after the aux cooler.
Everything is back in the truck and torqued down except for the secondary cat-pipe. I had two nuts left to tighten, but they got down to about 1/8" from the flange and stopped. Neither would go any farther. I tried to remove the nuts, but both studs just snapped right off. I pulled the pipe out and tried hammering the studs out, but they won't budge. Tried drilling one of them out, but broke off a bit when I stepped up to a larger size. Today, I get to try to press them out. Hopefully the pipe asy will fit in our hydraulic press out in the garage at work. Otherwise I'll have to take it to an exhaust shop to do it. Should be back together and running tonight. After all this trouble, the trans better work!