Progress:
Power door locks/remote are working (kinda important since I shaved the door locks).
Power window control modules are wired in. This... was slightly complicated.
So, I've talked about this before, but, these power windows have been an obsession of mine to improve since the start of this build. I'm using these, from Australia (like half of my car):

They basically just need a high amp power/ground, some switched inputs, and then they have an output for 2 windows per module (so I have 2 modules). The problem came in that they need a 12V switched input for signal. Seriously, who switches 12V for input? I didn't realize that until I went to build the harnesses. Not a big deal, except the BMW switches I use expect to switch ground. Now THAT wouldn't be an issue, except they use a common input for the switch control and the LED for backlighting. So if you run 12V to it, you now need to ground switch illumination AND your diode is backwards for backlighting.
So, I tore apart the switches and flipped the diode. I also needed to swap the illumination circuit to ground switching instead of 12V switching. That's not a big deal as the PDM in the ECU can sink to ground or run 12V, so that's just a config change. The only other thing on that circuit (illumination) is the gauges, which have 12V IGN already, so I just need to tweak the wiring on the cluster slightly to ground switch instead of ignition switch gauge backlighting. Also, when my gauges don't work in 2 weeks when I test them, I can come re-read this and remind myself I forgot to do that...

I still need to actually wire up the switches to the connector properly, but that's easy stuff.
Anyway, like everything, this took longer than expected, but the wiring is MUCH cleaner than the old 8x relay/4x circuit breaker setup I had, and the modules run the windows more smoothly as well, which is nice.
Next projects are fixing the gauge wiring, swapping out the fuel gauge for a voltage gauge in the cluster (fuel level is in the ECU and digital dash now), and wiring up the HVAC, stereo amplifier and center console bits. Hoping to get that work done this weekend, and get started on project "how the hell do I fit all this CANbus stuff in my "glovebox". The answer will be TIG welding and profanity, the volumes of each is yet to be determined.