vw manifold most likely not, you will either have too go with the ebay manifold (do a search) or modify your stock manifold, there is also the 666 fabrication manifold which is beautiful and woth every penny of its 700$ price tag but for a budget home brew set up its probably not what your looking for,
Intercooler- yes just about any stock intercooler will work, some more than others (supposedly the late 90s model saab ones are pretty good)
with the fuel system on a budget stock is okay up too 190 maybe 200 if your setup is very efficient (this is with a dead heading the fuel pressure regulator). above that (im not sure about them3 setup but im pretty sure it wont work and even if it would it would be pretty pricey) above that its pretty much new injectors and some kind of piggy back (smt6) or stand alone system
your probaly looking at anywhere from 600-2000 to do a home brew setup depending on how crazy you go.
also check out the turbo/ buildup section of this site there is a ton of info there