Success! Flashed and car started up fine. Ran VCDS, changed coding to manual, cleared codes, and no faults, ABS, ASR all good and no more complaining about TCM missing.
Throttle body won't align but that is a different issue. I did have one immobolizer error, but it could have been my fault, I had left the key in the ignition for a long time while I was reading. I pulled the key and tried again and it was fine.
Thanks so much! Going to do some more reading and see if I can successfully code out EVAP, SAI, CCV, etc..
Brendan