Sweet project. What panels are you cutting out? Unless you found that car at the bottom of a lake the only rust prone places are under the battery.
cslithergo and Mike, check out
http://forum.rennlist.com there's a wealth of Porsche info there.
As for running a built turboed engine, check the rules for the class you want to run first. If you're still set on building a turbo engine, start with an engine out of an originally turboed car, they use sodium filled exhaust valves and have some internal variations from the N/A engine. This also means that you would probably want to look at getting a 951 transaxle that has a bit taller gears and LSD. A good place to start on 944Turbo parts is
www.lindseyracing.com. And a good mechanical referance is
www.clarks-garage.com
As for running an LSx backed by a T-56, you'd really have to consider the class you plan to run in, not to mention you'd have to re-engineer the rear suspension. If you plan on going V8, keep the transaxle. Porsche engine's aren't all that fragile, but there are some things to watch for. The head is an interferance design and a broken timing belt will be expensive. The number 2 rod bearing is prone to spinning, but there are fixes to prevent this (refer to rennlist for details). Aside from this, the engines are pretty stout.
good luck.