The noise seems to be gone. I took it back to the shop and insisted that their certified Prius Tech take a ride with me. He heard the noise and agreed the noise should not be there. Apparently it wasn't the transaxle alignment. They never replaced a bearing when they did the suspension work. They replaced a bearing and noise is gone. The car now seems to be running a little more stiff (kinda like the parking break is on a little bit), but they say that will ease up as the bearing breaks in. So this is good news. The holes I found in the seat have been determined to be welding burns. They are replacing the seat cover. This all might turn out ok afterall. Still considering and selling my 05 to get an 06 if I can find a dealer that won't jack up over MSRP because I'm not sure my car will EVER be quite the same after 11k in damage. But for now, I'm almost back to normal.
glad you got the noise sorted out. the best way to get a problem solved is to show it to the tech directly. good luck deciding on the future of the car
Good for you. I didn't mean to be too alarmist, but I guess I was. You went at it the right way. A bearing would have been my second conjecture.