^An S54 6spd swap is easily a $10k job.
Honestly the first thing the OP needs to nail down is what he'd realistically be willing to spend. Earlier he said...
Originally Posted by Slowered318
I would like to obtain the turbocharger, exhaust manifold, plumbing and intercooler for somewhere under $2000. That leaves some money for electronics, fuel delivery, head gasket and to possibly upgrade internals down the road (maybe VAC or MM has something I will need).
So based on that I'm thinking his budget might be around $3000-$3500?
Once you know what you're willing to spend, then you can start looking at what your options are.