Fix one problem, two pop up. A reverse drill bit and extractor may work.

Was able to get it out, new bolt coming this saturday. I was able to get the car running when I installed the new waterpump, tensioner, and pulleys despite the battery being dead. I had a neighbor helping me and he commented that the idle sounds fine, but as soon as I threw it into gear, you can then hear a shift in sound with the problem appearing.

I've got a scanner but I'm not very well acquainted with it. The OBD2 codes so far were pcv unit, and misfire cyl 2 and 3

I've got the foxwell nt510 elite, I'm unsure if I could use this device to really diagnose what a potential issue would be.

You need to use that Foxwell in BMW mode, not OBDII. There are many codes that can show up that won't show up in the standard OBD codes.

Pull out the #2 and #3 coil packs. Swap #2 to #1. Swap #3 to #4. Clear the codes and start it. If misfires move to the new locations, the coil packs are bad. Mine had three different coil packs by 150k miles. All before I bought it. Three were OEM. I replaced all 6 with NGKs from Summit Racing. Plus updated the spark plugs to a single prong type. An ODBII scanner will solve this problem by moving the coil packs.
Even better, measure resistance between a non miss firing coil pack and 2/3. If resistance is way different, they are bad.

The scary part, they next to each other. Worst case, head gasket issues.

Good point. That's how I nailed down a defective coil when I had one. Went ahead and replaced all 6 since the truck had 160,000 miles on them and I figured the rest wouldn't be far behind.