I had a 91 GTI with an 8 valve and I know yours may not be exactly the same but here goes:
When I first got it, it wasn't running. I was told that the clutch was just done so I started doing a little research and it turns out that on that particular car, if you don't clean, clean, clean all the grounds, especially the one that hooks on the trans from the battery, it will fry the computer. Mine fired all 4 injectors constantly and thus filled the crankcase with fuel. Put a new computer in it and it smoked like a bitch for a few miles but ran fine afterward.
I also had an 86 GTI in high school that when I had the clutch done it had a similar problem where it wouldn't start and it was caused because it kept frying the knock box which is essentially the computer up in the cowl. I now suspect that it was a ground issue. I put a knock box in it and it ran for a few more months and then did the same thing.
Not sure if this is similar to your problem but I hope my terrible experiences help.