To update this one, the culprit was indeed the u-joint on the driveshaft. It took a while to get the new parts: the driveshaft had to be manufactured, was damaged in transit, had to get another one... took 2 months total. But hey, the noise seems to be gone and I had a loaner. They also did the front wheel bearings, just to be sure... and the steering wheel adjustment motor, because that was grinding.
The idle is still a bit boomy, though they said that is normal. Nothing really vibrates anymore, just a low frequency sound. I'm not sure it is normal (at least it shouldn't be), but after waiting a total of 3 months for this process, I decided to not press the issue and deal with it later. We'll see if it smooths out with time. Also, is a very slight whine normal upon initial acceleration in 1st? I don't know if it's from the transmission or engine, and goes away by 5mph or so. It sounds sort of like a Honda automatic whine, but quieter and higher-pitched.
I mean, I like this thing and all, but it doesn't seem quite as nice as my old G35S. Maybe it wasn't treated very well by the original owner.