Gt Tr3650 In Mach 1 Will Computer Work?

IMO swapping the PCM from the 2004 GT is likely to create more problems than it solves.

One other "possible" option to consider is going to car-part.com and get the correct PCM for your intended combination. IE Mach 1 with manual.

Here's some information on how you maybe able to perform a DIY PATS reprogram. Note, expect problems IF you live in a state with an inspection. The PCM VIN # will not match the car's VIN.

ForScan ODB2 scanner w ELM327 USB
https://www.stangnet.com/mustang-forums/resources/forscan-odb2-scanner-w-elm327-usb.57/

There are also many threads on how to convert an automatic to manual. Those threads will give the information on how to modify an automatic PCM to work in a manual application.

I believe the auto Mach1 has cast crank and the stick a forged one. The automatic was strengthened too.

Automatic mach 1s are kind of special. In the long term they will probably become more valuable than manuals from a collector's standpoint. There are many manual mach 1s out there to be had. Maybe just shop for the car you want and keep 1 more auto mach intact. Probably be a little cheaper buying a manual from the start anyway.