Got a response from Brendon at lt1swap.com, he runs a verification test to make sure the changes took to the PCM before sending it out. He reviewed the file for my PCM and it all took. OK, so its not the VATS.
I got out into the shop and looked over the engine and checked a few things he mentioned. All those looked good. I changed the wiring I was using to start it by adding a momentary switch so that I did not have to hold wires together. I fixed some obvious vacuum leaks. Tested the fuel system to make sure it was coming on briefly before starting. I noticed that it filled the rails, like it had leaked down while it has been sitting overnight. I did not have my fuel pressure gauge, so I could not measure pressure.
Cycle the fuel pump a few times to make sure I did not hear fuel rushing into the rails anymore and assumed that I had pressure now at the rail. I hit the switch and the engine fired up and ran. It settled in to a nice idle. I did not run it long since I don't have the belt (belt I got was about 2" too long) to run the water pump to keep it cool. Check out the short video...
Success!
That accomplishment made my whole day. I was starting to just say the hell with it and push it back outside and cover it up. Glad I gave it one more try.
I'll get a different belt on the way home today and see it I can get it to fit correctly. If I can, I will let it warm up and since it is still on stands, run the trans thru the gears to make sure that it turns the tires...
If it all checks out, I will fix the truck wiring so that I can start it with the key and get this front boot on Old Blue this weekend.
I just might get to drive this thing again for the first time in 17 years...