Not sure if this matters or not, but has the A/C Clutch Status (also seen it called Clutch Supplied Voltage) wire been added to the PCM yet? This is about the only "other" input that the PCM might need. Maybe the PCM doesn't know that the clutch has already been engaged?
A/C Clutch Status = C2(red) 18
This is wired into the power wire coming from the relay to the A/C clutch itself (+12V).
Aaron, thanks for all your hard work on this ... I am hoping you can get this worked out. I appreciate all the documenting you have done in this thread for the rest of us who are in the midst of LS1B swaps.