Just an update on this. Took it to an independant about an hour's drive from here. They seem to know what they're doing, their shop floor was clean and big and completely filled with exotics, I saw two yellow Ferraris, a 421 Cobra (don't know if original or AC, but this thing looked like it belonged in a museum) and lots of Porsches.

They diagnosed it as a bad thermostat and bad exhaust sensor, both of which are pretty much what I came up with after researching the codes and VAG stuff, so I wasn't surprised. There was no problem, as you guys stated, with the ECU.

The "tone" I had been hearing on acceleration was from a bad exhaust flapper valve (I had already figured that out as well, through advice from here and the ODB codes) so they're changing that. And good for them, that sound made me nuts.

I'm having them do the third tail light as well, I just want this car in as good shape as possible with no warning lights on the dash and everything working. The TPS system has been disabled at some point, I'm fine with that, maybe someday I'll put it back together, but whatever the previous owner did, it doesn't show up as an error on the dash, so I'm good with that.

While they are dug into the engine(s) to replace the thermostat, they also suggested I replace all spark plugs, since they're already in there. Sounded like an upsell that made sense to both of us, so I agreed. Can't go wrong with new spark plugs on a 65,000 mile car, but then again, this isn't my 1970 Triumph with carburetors, so this is probably only going to make me feel better instead of really making any kind of difference.

My only complaint is that in this economy, like my stereo installer, they are crazy busy and backlogged: they made me wait two weeks for an appointment, and now the car has been in the shop for three weeks and I still don't have it back yet. I suspect the dealer would have charged me double and found more stuff I "needed" to fix (this shop doesn't seem to go that direction, they could have force-fed me an ECU if they were into gouging) but I bet I would have had it back in less than a week, maybe only three or four days. So that's quite a trade-off.