I've got some Issues... well not me, but my car!

Hyup, I'll go with @TrailBeast on the driveshaft thing, instead of bent. It helps explain the hop when it first starts to spin, which I wondered about, but it didn't connect inside my brain.
The EGR remark was just a poke at the sound of the idle. which is a normal function of a performance cam at low rpm.
But I'm sticking with a noisy pinion bearing.
As to the flapping, I wouldn't want to place any bets on that; but I would hold off on the diff inspection until after the U-joint is looked at.