Providing some background information on the adventure I've had during the Focus ST225 Swap on my wagon,

I chose to go with the following setup,
- Front: ST225 Caliper, Stoptech Rotor, Stoptech Pad, EBC Stainless Line
- Rear: Stock Caliper, Stoptech Rotor, Stoptech Pad, EBC Stainless Line

Swap was done but bleeding was an issue. The shop I enlisted to do the work, managed to bleed using a air pressure bleeder after the manual pedal method.
During that time, the master cylinder went bad and was replaced.
On the test drive, the brakes were hard and eventually bound up. It was carefully driven back to the shop, short 1/4 mile distance.

After that episode, the ABS Pump was replaced. Now I am facing the following issues and codes:
P1637 CAN link engine control module/ABS control module circuit/network malfunction
P1799 CAN transmission control unit/ABS control unit circuit malfunction

ABS Light on and Gearbox Fault on the dash. The car is most likely in limp mode and possibly stuck in 4th gear.
The TCM was replaced with a used one that is Plug N Play. The ABS Module was tested for proper ground and voltage, it has pased.

The ABS Module was rebuilt through UpFix but, the issues are still occurring so I am also working with them to see if it needs to be checked again.

My question is, is the ABS module toast after all this? Also, if I do need another module, would it need to be programmed by a shop or dealer?