Update: With the wiring finally done I tried to start the engine but it would only fire and die. The short version is that I ended up getting the PCM checked and found the VATS was still there even after I had it reflashed with the harness rebuild. This local shop that checked it removed it again and I reinstalled the PCM. The engine fired immediately and ran until the fumes gassed me out of the garage!
https://youtu.be/hqQXh4AXnQ0
Then I worked on a few other things including finally getting the radiator hoses situated and filled the engine and radiator. Then I tried to start it again and now it turns over but doesn't fire or run. The setup is a 2006 LQ4/4L80e with a refreshed stock ECM. No mods except the new air inlet, Hooker cast headers with the first couple of feet of exhaust tube bolted on, no mufflers, and the O2 sensors that came with the engine are inserted in the exhaust pipes and connected to the harness.
Ck Engine light is on and I pulled the codes: P0036 P and P0056 P - both of which appear to be O2 sensor issues for each side, plus P0452 showed up and then disappeared which is Evap Emission System Pressure Sensor Low Input or Fuel Tank Pressure Sensor issues. With the swap there isn't this type of sensor any longer that I know of.
None of the O2 issues appear to prevent a start? Any thoughts?