Update:
Started the last bit of wiring removal - the stock charging system. I got everything separated and removed the starter wires:
Took a break from wiring while I wait to get my gauge issue sorted. In the meantime I tapped the back of the water pump housing for the sensor for the water temperature gauge. Between the stock unit, the gauge and the ECU I'll have three water temperature sensors on the engine, LOL.
Next, I got tired of trying to envision everything in my head so I had a bit of an idea. Why not use my old parts to build a dummy engine?! After some screwing around this is what I was left with:
So now everything is routed down the driver's side. I'm trying to think of a way to route all the new engine control stuff on the passenger's side but I've got nothing that doesn't look weird or run wires perilously close to the exhaust manifold. At least now I can start wrapping everything back up. When I'm done I'm going to have three distinct harnesses in the engine bay: front (lights, sensors, etc.), engine (coils, injectors, etc.) and charging (alternator, starter, main fuses).
Speaking of gauges, here the pods I've been working on. Bolts right to the stock console and fits perfectly in the stock double din location. I'll eventually figure out how to put the aftermarket single din back in there...