Help! Tranny problems revisited.

OK, July 2001 I had the tranny rebuilt for the 2nd gear grind at 36k. I had just bought the car and had to fight to get it done because I had cut the shift lever down and they wanted to blame it on that. Well it was finally done as a one-time "goodwill" fix, approved by the local VW rep.

Fast forward to present day, car now has 41k on it and I have a new issue. A strange thump that usually happens when you come off the gas in 1,2,3 gears. The dealer has had it all day and found nothing else wrong and are now leaning towards an internal tranny problem though they don't know what. The car is now lowered, intake, chip, and a couple other minor mods. Do I have any recourse in this case? It sure seems like the guy either screwed up in the first rebuild or did not replace a part that may have been worn. I know trannies are complicated to work on and I really don't relish the thought of eating the cost of a new one. The car is at a different dealer but in the same area so I am sure it would be the same VW rep. as last time. I know I want a technical explanation from them if they try to deny the fix because of mods and if they do fix it I want a new tranny, not another rebuild.
I appreciate any helpful input or similar experiences.