I'm in the same boat. I picked up a good condition 99% stock (just stereo mods) 89 Si this past summer. My intent was to keep it stock because it was just so OEM. I then decided that I would swap the suspension from my other modded CRX that I autocross. I then sold that CRX to a friend and decided a few weeks ago that the A6 was tired and now I'm working on a swap.
My thought now is this: Although it would be great to keep it stock because they're becoming rarer, especially unmolested, and would have better resale value...it's my car and I need more power. I don't ever plan on selling it, so resale isn't really a concern to me. Bring on the powa...do the swap...do it right...keep it clean.