Well, it looks like this ordeal is actually going to be over rather more quickly than I thought. I took the camera and lens to Colonial Photo and Hobby in Orlando. Apparently they have significantly upgraded their repair facilities. I got a call from them that they could fix both in house. The camera is already done and back with me, and the lens should be done in about 2 weeks (depending on how fast they get the parts). That's a lot better than the 4 to 6 week estimate if I had to send it in to Nikon!
When I talked to the repair tech about what he did to my camera and my concerns, he said that he had taken it apart, fixed the broken stuff, completely cleaned the inside and sensor, and hooked it up to his diagnostic equipment to make sure the lens mount hadn't been shifted, and checked for back and front focus problems. It may have been an expensive service, but it feels like I got something for my money.
If anyone has a hankering to browse a brick and mortar store while in Orlando, I highly recommend this place. I had to get out of there quickly when I picked up my D90. Behind the counter I saw many D700, 85mm 1.4, 200-400mm, and many other equally enticing boxes.
They were also able to identify an old lens I got from my uncle as a Nikon Ai lens that I can safely use on my D90. So now I have a fully manual 50mm f1.4 lens to play with.

This should be interesting, as it won't meter, so it's guesswork and checking the histogram.
Erich