Hi bud, I don't know what's causing your issue but there's a good faq for removing the tranny if you haven't already seen it but it might be better to wait and see if someone else can give you info on what might be causing the problem.
http://www.myturbodiesel.com/1000q/a4/a4-ALH-TDI-engine-index.htm
http://www.myturbodiesel.com/1000q/a4/a4-ALH-TDI-engine-index.htm