Big Sky Euro

No need to replace the crank shaft or the cam (although a different cam will give you some performance) The valves can be replaced, only necessary if they are bad or again for more performance. No need for new pistons you can replace the rings as long as you aren't boring it out. As for the tranny we can diagnose that first.
I am coming home soon and I have the number of a guy (Matt @ UPT) for you to discuss your build with.

I agree with josh here - but I would only add that you should pull the entire bottom end (including both ends of the con rods) and have it mic'd for tolerances. Depending on the condition you may need to go .10 over or more, and possibly need to recondition your con rods - if they are in good shape and can be reused. That would save you some $$, while 'doing it right' the first time. IMO you won't need to touch the head if it is in decent shape, but if the seals and/or guides are out of spec, or you plan on going with a hotter cam you should get an entire rebuild on the head. That is a 16v - 2 intake/2 exhaust on 4 cylinders.

Most of what you need to do depends on how well the PO was up on oil changes and maintenance.

How much of this are you planning to do yourself?

vw cranks esp 16v ones are bulletproof, my engine had WELL over 200k on it and the crank was in spec and didnt even have to get larger bearings. on top of that the journals were perfect nothing needed. get the head rebuilt, for 250 bones i got new valves a deck polish, all new valve guides, a 3 angle valve job and a rediculous cleaning. no reason not to for that money. check the IM shaft bearings too, they fail before anything else does!