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I live in upstate NY (Albany area). I own a 2003 base. I dont believe there are any reputable specialty shops around me that could swap out my clutcth, diff, and torque tube when the time inevetibly comes.
Does anyone here know of any shops in this area, or the surrounding area who could ace this job?
Try attending a local Auto X or Road Course event. The C5 is a VERY popular platform in these activities. You should be able to makes some good maintenance connections and it will be a fun day. Before I decided to participate in these activities I treated them like a car show where the owners actually put their cars capabilities on display. WARNING: You too may get hooked and the next thing you know your "baby" is gutted, caged, and trailered back and forth to events!
Albany isn't exactly "upstate" my man - you're kinda in an extension of new england geographically speaking, so that being said I can suggest a couple companies I know of within 3 hrs or less of you that are very experienced & fully capable of handling this job
#1 Slowhawk Performance in Bridgewater, MA - just under 3 hrs from Albany, I have been bringing cars to Don & his team for over a decade & have always been satisfied - even when I had some issues on a recent big build/project (engine had to come out 2nd time post SC install, & had an issue w/ the pilot bearing on my clutch he wound up taking care of the last remaining issues labor free, just charged me parts) These guys are LSx gurus, do custom turbo builds, engine swaps, heads/cam swaps, full teardown/rebuilds, old stuff new stuff, superchargers etc etc etc - great tuner, won't push you into adding stuff you don't need, if you call em tell Don local Matt w/ black C5Z says hello!
#2 East Coast Supercharging - while I don't have firsthand experience w/ them wrenching on my car, I have been to the shop & talked to the owner(s) previously & got a good feeling from them. Their rep is very solid & I personally know people who have had their cars heavily modified by them w/o issue, Slowhawk is so close to me though & I already had a relationship w/ the owner from previous builds so I decided to stick w/ them