IMHO the 99+ years are way nicer cars than the under-99 models. They are made with much higher quality interiors and more consistent manufacturing means less stupid problems. But they are heavier and the suspension is too soft but since you are going to mod it anyways that shouldnt be much of an issue. But it sounds like you are looking for a high quality road car so I think you might appreciate the higher quality of the newer models and they also have the cool blue gauge and dash lights.

And if you are interested I have a 99.5 Golf 2-door for sale. It only has a 2.0 liter but if you are looking for a very nice used car you can do an easy swap and save a lot of money over buying a new one or even a used 1.8T since they just started offering that last year. Mine is in excellent condition its just kinda slow... lol...