If I were in your situation I would do one of two things:
1) Pull trans and send it to Stasis for a rebuild. While expensive, you know it will be done right. And if there happen to be any problems with the rebuild, Stasis always stands behind their products so you wont be left out to dry. For a big, high cost, project like a tranny rebuild I would rather pay more for it to be done right, by a repitable, well established shop.
OR 2) buy a used trans from a junked S4, A6 or Allroad. In the end, it would probably cost less than a rebuild and you wont have any downtime since you could just swap in the new one (assuming your car is still drivable now).
The route I would go would depend on finances, time and if I want mods done to the tranny while it's out. But #2 will probably be the cheapest and easiest, assuming you can find a working trans for cheap.
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