Welcome to the website!
It never rains, but it pours... eh?
First question: will you be doing the repairs yourself, do you have access to a TDI-expert mechanic who's fairly reasonable in his charges, or will you be going to an old-time VW shop or dealership?
Considerations: The 2004 will not only need a new turbo (not easy to find a good used one for that vintage - and this is assuming the engine didn't "run-on" on the oil in the intercooler and got hydro-locked), but given that they have camshafts that are known to wear - meaning that you'll also need to get a new camshaft, but lifters as well... I'm also assuming it now also needs a timing belt... Still, if you're doing the work yourself or have an affordable expert mechanic, it's still a nice car!
The New Beetle: a new clutch kit (G60/VR6 single-mass design is preferred) isn't that expensive, and shouldn't cost that much to install. However, if you're doing the work yourself, the cable adjustment on those DQY transmissions is rather tricky.
Please update your profile to better indicate your location... (Texas is a fairly large state, as I recall...) There may be someone local that we may (or may not) be able to recommend to help you out.
All the best,
Yuri