About 6 months ago, I hit a pothole in my E63. Afterwards I had a bad vibration, the wheel was bent out of round - ugh. I replaced the wheel.

Vibration continued. Shop said, get new tires. Did that. Still vibrating. Rebalanced the wheels, that helped a little.

But I am still getting a slight, but noticeable vibration that starts at about 50-60mph. I have had the car in about 3 times now, and I feel like I need to direct them to specific things. It doesn't seem like an engine mount issue, since it only happens at speed. The vibration is not huge, but enough to be irritating.

Any suggestions here of where to direct the shop?

Get an alignment. You may have bent something in the suspension, and get the tires road force balanced under 20 lbs, ideally under 10 lbs. I'm just assuming that your shop only spin balanced them. Road force balancing is an additional process that applies pressure to the tire via a roller to simulate the road and measure high/low points and then tells the tech how far to rotate the tire on the wheel, so the high points of the tire get aligned with the low points of the wheel, so that the final assembly is truly round. If they can't get it below 20 lbs, then the wheel and/or tire are too unround.

Dd you have your suspension components checked out ? Something could have damaged.