Alot of the auto trannys have problems as far as I know the only problem you may have is your shift linkage If you do a manual swap unless mark4 2.0s are hydro but basically if you want to be on the safe side I'd do coils and wheels and do your motor slowly so you can make sure it's exactly what you want and it's problem free. And do a manual swap at the same time. If you got into this car hoping it would be fast for a low price I'm sorry but that probably won't happen. You can make power out of a vw but it tend to be a little more exspansive and if you dnt do it the right way you'll have lots of problems down the road so you might as well do it the right way the first time. I've learned this after tryin to rush a couple projects. But like magoo said I think a 1,8 with some bolt ons would be the way to go or a full build if you have the time and money. But do wheels and coils first your car will look way better