I see a trned here. Jetta TDI owner here too -- can't recall year, but mid/early 2000's. Before the blue-tec debacle. Great car, manual transmission -- which seems to be pretty solid. But every person I knew who had an automatic had trouble.
A friend at work went through 4 transmissions --- fortunately, all warranty. 'Dub was like "we've never seen this before!" -- he was in the "Oh yeah? Go to this forum...."
The only trouble I ever had with it, was randomly it would not start...Had to open the hood, and I found a silenoid that didn't open reliabley --- on the firewall, on the passenger side...flip it and the car would start right up. Every time. To this day, I don't know what the name of the part was...but it worked, I knew about it....
Loved that car until the timing belt broke...left me in the middle of nowhere. Quite literally. County road, top of an off-ramp in a wide area where trucks sometimes park overnight. 1 street light, very weak cell service (1 bar, if I stood on teh roof of the car, and put my right hand into the air kind of service) at 10:00pm on a friday night.
Had enough "juice" in the cell battery to make 1 call --- fortuntaely a B&B I knew about was about 10 miles away, I called and pleaded for help....they came and got us. But it was sketchy.
Loved that car