The PCM from the other EX is looking for a PATS signal which its no longer getting since the module is unplugged. Even if you did plug it back in it still would not function because that PCM is not pair to your PATS Module. I would swap in a Truck PCM, leave the PATS unplugged and see what happens.
On my 01 EX I swapped the engine harness out for one from a late 99 truck with glow plug relay. Initially I didn't have a chance to swap the the PCM'S also, so I ran the EX PCM with the truck wiring (and PATS plugged in). The EX PCM controls the regular relay just fine (but has codes). Eventually I swapped the EX PCM for a "CKX0" DPc-422 PCM from an 01 Truck. This took care of all my codes but I then started getting a the Flashing PATS light. I unplugged the PATS module and bam no more irritating light. I ended up with No more PATS or PATS light, no codes and a replay instead of a GPCM.
Oh and I didnt pay Ford to flash anything. It was all plug and play. The EX PCM and PATs module are what need to be sync'd. If you swap to a truck PCM and unplug the PATS then nothing need flashed by Ford
If you end up needing a EX PCM I have a perfectly good one sitting in my attic that I'll definitely never use again.
David