Appleslicer-
First you must understand that Mark and I are old friends. We both are subject to over engineered solutions just because we think it's cool. This leads to ongoing jokes about stuff like "I checked the oil and it was a little low so I went ahead and overhauled the engine, used a new callies crank and had the heads max ported. Maybe the oil will be ok now". A lot of people on HybridZ call it "while I'm at it" disease.
Generally trans alignment isn't a problem with T56's and LS engines, I wouldn't even worry about it. It's difficult to check with the T56 bellhousing arrangement, but I've never known of anyone having trouble. I used to run a TKO in my car, and they are much more sensitive to alignment than 56's. I posted a write up about centering the bellhousing several years ago if you want to hunt it up.
Sorry to cause you to have second thoughts. If the trans went together smoothly and the clutch works OK, I wouldn't worry about it. Most likely you just got a worn out trans, Been there/done that too.
John