What other modifications did the engine have when it was running the PFC? I assume when you swapped back to the standard ECU that all other items are standard too (injectors, AFM, etc. etc.).
If its seemingly an issue once a bit of temperate is involved, ensure the IACV is working correctly and connected correctly, these are failing more and more these days due to their age (is it the same one that was on the previous motor?).
You've already tried CAS, which would have been my go-to first as well.
The water temp sensor for the ECU will also cause this, again, is it the one from the previous motor? Swap that with a known working one too, these are available on EFI Solutions new (or elsewhere, they're generic).