I wholeheartedly second nubcake's response. "By the book" is crazy expensive. Even doing stuff yourself can be expensive until you have worked on it a bit and get to understanding the car. I have now pulled an engine 4 times and reinstalled one twice (today/tomorrow will be the third, and the fourth was a part-out). The fourth engine pull took me about 6 hours, mostly by myself but with a little help from my brother when actually removing the engine/transmission.

The auto transmission is a known weak link, but I see nothing wrong with your idea to buy one, drive it till the trans goes or you get tired of it (my first one went, my second one lasted 1 month before I got tired of it). As for the shocks, there are plenty of folks on this forum who seem to have good feedback on Koni sport shocks with the factory springs for an inexpensive option, or KW's if you can spend a bit more. Engine wise, my impression is the internals are pretty bulletproof as long as you take car of them (standard maintenance). There have been a few reports of plug threads stripping and causing damage, but other than that I can't think of any common issues.

As for miles, I tend to drive my cars a fair amount, and I would agree too that at 100-130k there's a lot of life left, provided the car was maintained for those miles. Definitely make sure any one you buy has been properly maintained. If it hasn't, catching up on the maintenance could quickly double the cost of the car.

Timing belt can be done for much much less than list price if you do it yourself. The last one I did cost around $550 for parts, but there are even better options that I've come across since then. $550 spread over 40k miles isn't really all that bad.

If anything else goes wrong, just ask on the forum here. Chances are others have run into the same thing, and may have found a better way to fix it than just buy and replace parts.

And finally, if you do get one, you're right up I5 from me. If you end up going with a manual conversion, feel free to get in touch. There's a few of us around here with RS6s, and at least one other (GreggRS6) who have gone through or are going through the swap.