First things first: It only 'clunks' between D&R and only when the engine is warm? That could be motor mounts or you need new tranny fluid. Flush your tranny with new fluid, then if there is still noise check the mounts.

Second: I assume you went to a dealer for that kind of price. But even 10 hours of labor is a little high. The 1300 for a rebuilt tranny is about right if they guarentee it for a year.

Third: If you have to get another tranny, get one from a 1997. It's the best year that will fit your car.

Fourth: Stop going backwards real fast and shifting into drive with the foot flat on the floor. It makes for great tire squeal and black marks, but does a number on the tranny. :)
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95 854T, 88 780, 88 245, 01 A4 Audi