I started out with a 1997 model for which I overpaid somewhat; it was in mostly-good condition in spite of having been backed into a tree, and I drove it home without incident. It was leaking copious quantities of transmission fluid, though, mostly from the pan itself. After some trials and tribulations, I got that car in fairly good shape, but then it started flaking out on me again. As it turned out, the cam position sensor had broken, though I didn't actually discover this until I started tearing into the other vehicle.
At that time, I was offered a complete, running 1998 model with several systems working which were malfunctioning on my vehicle. For example, the solar sunroof was working properly, because the blower motor had been replaced, and the engine was running well. The major problem with the vehicle was that the transmission demonstrated the classic symptoms of Clutch "A" basket failure. This consisted of slamming into drive and then lighting up all the gear selector lights at once, starting in second gear, and refusing to ever lock the torque converter. I drove it home over the Hopland Grade like that, on a trip ticket. Today that would probably be impossible, because there are numerous places where it's one lane only and you can't start uphill in limp mode. I also couldn't go over about 55 because the vehicle would start shaking like mad, as if the various bushings were all shot. They were.
After looking the car over well, however, I decided that it should really be the one to take over. The body was cleaner, the paint nicer, and the interior much cleaner. The stereo was a Concert I, rather than my ancient Delta CC, meaning that it was much easier to get aux input. I had keyfobs, not just keys, so I could use remote entry with my key blades — it's much cheaper to buy new fobs and swap your key blades than it is to get Audi keys cut. And the lighter paint color (alusilver instead of the darker silver black color) is less susceptible to the effects of weather.
So, to the task. To make a fairly long story short, I built a wooden gantry and used it to swap the engine and transmission from one vehicle to the other in spite of not having a concrete slab to work on. I had done the timing belt job on my 1997's engine, including every oil seal except the rear main seal (which if I were smarter, I probably would have replaced during this job) and the water pump. This engine has around a hundred thousand more miles than the engine I took out of the 1998, but it has good compression and I have a certain attachment to it since I've done both head gaskets and can be reasonably sure that they aren't going to leak.
To solve the problem of going mad over 55, I swapped over all the front suspension links. They are Chinese (Deutsch-Parts) except the lower front "track links", which are OE (TRW). It is by far most important that they do not fail, and they are by far the most fiddly suspension link. The next biggest problem, which I've only just solved, was with the brakes. The right front wheel was hopping on braking after driving on lumpy roads, which is pretty much all of them around here. While I was trying to solve that problem, the brakes all but locked up on me coming over the Hopland Grade. As this was fairly frighteing, I went full nuclear; I swapped the right front shock, right front brake caliper, brake servo and master and replaced all the brake flex lines. In the bargain I got a full brake fluid flush.
Another big problem with the vehicle was that it had a fully cracked windshield. I replaced it with a piece of Pilkington glass, which is a solar-laminated, solar-coated, green-tinted job much like the original. The rear window is also broken, and I hope to swap this from my parts vehicle. Otherwise, I'll probably pay someone to pull me one from a pick-n-pull.
Now I was down to trivialities. The prior owner had chopped out much of the stereo wiring for the purpose of running an aftermarket amplifier. I cut the matching section out of my 1997, then soldered it in and swapped my Bose amplifier over. I added an AUX input to the Concert I stereo using an Arduino, and installed a Panavise mount with a RAM X-Grip for my phone. I'm still trying to come up with some graceful way to get a small computer into the vehicle; the current contenders are a low-power Dual Athlon 64 running Linux, and a Pine A64+ running Android.
It looks like I'm down to just minor issues now, finally. I just put in fresh coolant; I am running Pentofrost SF, which as far as I can tell is the last remaining honest-to-god VW G12+ coolant available in the USA. This is the first generation of pink stuff, and it is a no silicate phosphate-based coolant which must be installed with distilled, RO, or DI water. I need to replace the front window regulators and fix the sunroof since they are all clunking while operating. All of that is good in my old car, and I'm hoping I can swap in its rear window, as well. I put some scratches on the fenders while reinstalling the hood and have to get a spray can so I can fix those. But all in all, the car is in good shape, except for an extremely loud fuel pump which is probably also going to have to be replaced very soon.
Now if I can just get all the gas through it and slap some fresh premium in there and run it for a while, maybe I can try another 0-60 run. So far, my best is 8.4, which is almost two seconds behind spec...