JBsC5,
The example you cite in your post (selective swapping of rear end) is precisely the reason that I am attempting to get a statement in writing from GM regarding the affect on the factory warranty if I were to add LS6 parts.
I had seriously considered getting a Z06 prior to the post. However, after driving one for about 2 hours in various traffic conditions (with a fair amount of stop-and-go traffic), the next day, I was hobbling around with tendonitis in my left knee. At that point, I started thinking about how I could get to an "almost Z06" in the coupe. Based on Hib Halverson's post on the F55 suspension, I was very interested in the F55 option for the coupe as well. However, given the expense of repairs to the F55 suspension, the last thing that I wanted to do was proceed down a path that would void the factory warranty.
I am presently at the stage where I am working with a dealer to get written clarification from GM regarding warranty coverage for LS6 parts installed by the dealer prior to delivery. If GM vetoes the LS6 parts add-on idea, then I will be looking very seriously at buying used and sending the car off to Mr. Lingenfelter for some tuning magic. I agree with you about the state of the used market. There are some very good cars available for very reasonable prices as a result of the zero percent financing programs offered by the manufacturers.
Thanks to everyone for their comments and ideas. If anyone else has a comment/idea about how to proceed, please respond.