Picture-free update: A frustrating evening last night but could have been worse. Soooo instead of using a pre-wired harness I figured the uniqueness of this meant I should wire everything up myself. So I ordered the pots, switch, etc. (the ones that I "dry humped" in the last post) and when the pickups arrived last night I got to work.
Once you get past the mini switches the main guitar controls are actually wired up normal. All the funky stuff happens at the mini switches. This will be important later.
So I wire it all up and... the bridge pickup works except the tone knob is working backwards. But the mini-switch to split the pickup is working. The neck pickup however, there is no sound,. And the neck pickup is the one that has both the coil split and the phase thing going on. So of course my first thought is "well I must have wired the mini switch wrong" so I redid the phase inverter switch and still nothing from the neck pickup. So out comes the multimeter and everything looks right until I get to the neck volume pot. I think either it was bad or I fried it because when I took the output from the neck pickup and wired it directly to the jack everything worked as expected (even the phase switch).
So long story short I actually DID wire the mini switches correctly and rather than try and swap out parts and troubleshoot any more I just went to Gunstreet and ordered a standard SG prewired harness. When it arrives I should be able to just hook the output from the mini switches up and be good to go. Then it's strings, a setup, and a demo video!