Very weird transmission(?) issue, wondering where to start
 

So I'm not sure if anyone has ever encountered a problem like this, but maybe someone can point me in the right direction to fixing it:

I bought a '90 Turbo GTU a few months ago, but the previous owner had removed the turbo, leaving all the other parts set up for a turbo that wasn't there. I initially worried about the idle being set up too high, but figured the transmission would be fine, and I'd just have slightly inconvenient gear ratios. I'm not sure if any of that contributed to my problem at all.

The check engine light came on when I was moving through slow traffic a while ago. Suddenly, I was getting almost no power in first gear. The revs climb, but the speed takes forever to get going. I'd inch along, it was like there was some kind of disconnect between the engine and the transmission. This continues to happen, although sometimes first will be fucked up and second will be fine, or they'll both be messed up and third will work, or first will be good and the rest will be problematic. It's never constant, and it doesn't start until I've been driving for a good 15-20 minutes. It usually starts with the check engine light flickering when I shift, as soon as the knob hits neutral or moves through it going into another gear.

This is bizarre. I'm afraid of having to replace the entire transmission. If anyone has any suggestions as to what specifically could be wrong, or what could have caused it, let me know.

You have an S5 so the first thing you should do is dump out the CEL codes. That could point you in the right direction. Sounds like the car is going into limp mode. Check compression, check for clogged CATS. It will probably be a search mission because there are a lot of possible causes that could result in the symptoms you've described.

Your clutch is slipping. Either worn out disc or glazed pressure plate/flywheel/disk. In a 5speed when the car is in gear if your revs are moving disproportionally to the car speed the clutch is slipping.