It sure would be helpful to mention this is NOT a straight forward Cobra swap. It does complicate things that the donor car was a V6.
There are a number of differeces between the V6 and V8 in body harness and electronic sub-systems. The effect of those differeces depend upon the EXACT combination of original car, donor car, and which wiring harness has been retained and which have been swapped.
If the CCRM makes a single "click" when the key is on, that's likely OK. If the CCRM makes a "buzzing" sound or repeated clicks, that's a problem.
I'm sorry. I thought this was a SOHC to DOHC swap until I went back through some of your old threads.
Expect some issues mixing a 01 PCM with 03 cluster. Plan on comparing pin by pin the differences between the MY's cluster.
2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.