Update on the "clunking & thud"
Well, it took a while for me to find the time to schedule the service appointment - my dealership is an hour from home - but I have it all done.
They replaced the drive shaft and everything seems perfect. They also replaced the door seals, but I will need time to see how effective that fix is.
Interesting though, the service manager I dealt with the last time is no longer there; I was told he was "doing things on his own too much", such as ordering replacement parts due to TSB's! Oh well, I'm glad I got mine. The new manager said that they can't just go ahead and order things like the new door seals unless a customer complains... I told him I DID complain, but I did it nicely.
Total bill was $0
I wonder what the price tag is on a new drive shaft?