Ok, found the issue! Not sure its 100% corrected, but found a big problem that when fixed seems to have helped a lot.
1. I'm running a Right Stuff rear disk conversion - It's essentially the factory setup used on the 2nd gen TA's with GM calipers.
2. I'm running an original style master cylinder - it is supposed to be compatible with the Right Stuff setup.
3. I'm using a 4wdb prop valve from Inline Tube - it is designed to work with the original master cylinder.
So I found a few problems so far.
1. The rear caliper bleed valves need to be cracked more than a 1/4 turn to get fluid through them. I was trying to both pump and pull with the vacuum pump through the bleed valves with only about a 1/4 turn. I was pulling air through the threads, but not actually pulling any fluid through. The bleed valve needed to be turned almost a full turn to get fluid through it.
2. When I bled the front brakes the bar in the proportioning valve cut off flow to the rear brakes since the system was completely dry and there was no fluid in the rears. I had to reset the prop valve bar by using a pick to recenter it through the switch hole. I then purchased a tool off of Amazon that would hold the bar in place. After that I was able to push brake fluid through the prop valve with a syringe, but still wasn't getting fluid to the rear brake lines when pumping the brakes. Here is the tool:
https://www.amazon.com/gp/product/B09G68TRKT/ref=ppx_od_dt_b_asin_title_s00?ie=UTF8&th=13. Whenever I installed the MC on the brake booster, I was not able to push fluid to the rear brake lines. I loosened the MC and verified that the Brake Booster push rod was engaging the MC slightly when I would tighten it down. I checked the push rod on my original booster and verified it was the same length as the one installed in my new booster. It was. However, the push rod was deeper in the original booster by about 1/8 of an inch. I was perplexed. I messed around with the push rod in the new booster and found that if I rotated it slightly while pushing it in, it fell into place. I believe it was notched in a way that the bottom pin actually had to slide into position for it to go all the way in. Guess what? That corrected the problem with getting fluid to the rear brake lines. After that fix I was able to get fluid to flow all the way through to the rear calipers using the syringe and pushing it through the opening in the rear well of the MC.
So I think I was dealing with a number of problems. The biggest being that the MC was partially engaged and not able to pull fluid down into the rear position since I was not getting full travel of MC piston. Hopefully this fixed the problem. I still have some air in the rear system that I'm working on correcting, but the brakes seem to be functioning now. What a PITA this effort was. Granted I've never done a fully dry brake system before either.