Quick update, Sorry for not responding or updating. I sold my Mustang and took the Golf to the same shop I had flash the tune 2.5 years earlier. I asked for a laundry list of things to be looked at, then went out of town for a few weeks for work.
The shop diagnosed the loss of AWD as a faulty transfer/bevel box. They replaced with a used S3 unit.
Other work included a DSG fluid flush, motor mounts, Cam cover oil seal leak, Haldex fluid flush and new pump (even though I specified I had already done this twice), they took my golf to the local dealership to have the new pump coded (I assume a learn cycle?), and completed an oil change.
They did not address my requests for the faulty exhaust flap motor connectors, the driveshaft dampener, the Infotainment swap (currently displays 'offroad' and I wanted 'performance' gauges) or the bearing noise in the transmission.
I picked up my golf, we discussed what work had been completed. I received a discount because I paid in cash, and total OTD $5400.
It was pouring rain on the drive home so I just drove cautiously and parked it for a few days. Finally a good weather day arrived and I went for a drive. I gave it some throttle in sport mode and noticed a bit of traction control light flashing. Thinking it was cold tires I drove a bit more to warm them up. I disabled traction control, and stability control, used both feet to take a screenshot and when the revs stabilized at 5k I side stepped the brake. it pulled hard for 10ft then AGRESSIVE wheel hop.
I was crushed. I called the shop and explained what had happened. They told me that these cars always slip a little and to leave traction control on. They said they would warranty the transfer box but I would need to cover labor for replacement.
Broke, angry, and defeated I drove around in fwd for about 10 months. I finally scraped some money together and found a sketchy looking site (Automotix) with equal parts 5-star and 1-star reviews that listed a few transfer boxes (no pics) for MK7R. I read a few of the one star reviews and it seemed like most of the issues were around shipping delays and trying to return items that the buyer ordered incorrectly. Of the 4-5 I picked the lowest mileage box and paid $350 plus $180 freight shipping. I asked if I could just pick it up as it was listed as 90mi away but was told that wasn't possible. Alcohol and depression helped me click "buy now". The part arrived at my office 3 days later and the S&R guy sent me a picture as I was out of town. I immediately thought there was a problem as the only exposed part showed a hacked pipe sticking out of the wrapping.
Once I actually saw the part in person i found that it was the rear driveshaft flange where they had cut the driveshaft instead of unbolting it. I took a weekend and watched a few Humble mechanic vids, along with some other pics and posts. aside from the two top bolts being absolutely impossible to see and taking about 60min to get started the process was somewhat easy.
After almost two years I have an AWD Golf R again. I have not launched it yet, but aggressive acceleration, going full throttle while in motion and general lack of torque steer tells me everything is back. No wheel spin or TC light.
Summery, I trusted the shop and employees I worked with originally. I should have run away when management and employees changed at that shop. I now have an old transfer case that failed. A friend has a bridgeport mill at his house and we are going to attempt to slot and key the ring gear to the shaft. if that isn't possible we'll weld it and then I'll have a backup for when the installed transfer case fails.