quattroworld

That said, I will play devil's advocate. Working with engineers everyday I've been groomed to analyze cause/effect and not to change 3 factors and expect to understand the results. Unfortunately you did a TON of work at once (which is the way to do it in this case) but the net result is you are having a problem and it could be a "new-bad" TC or it could be the result of any number of (or combination of) the other repairs/upgrades/changes you made. I'm not sure you could confidently say it's the TC without putting your original back to to confirm. Something that would obviously be a giant PITA.
Over the years of Audi ownership I've read/heard that some people love Advanced and some people loath them and refuse to do business with them. So not sure if it's about catching them on a good day/bad day or what.
As far as the basic health check, there's at least one (if not two) green check valves on the top of the intake manifold. You should check to make sure they're working properly. No idea how that could relate to your problem but I had a bad one on my car when I first bought it. Found it when I did a complete test of my car. If you have vag-com you can do a throttle body alignment as well. Again, no idea if that will help, just something to try.