Completed the main wiring harness. I decided to not make a secondary harness for all the aftermarkets additions, and just wrap them into the main. Here is a list of the modifications I did;
-Repaired all 'tap' splices by cutting wire and repair with heat shrink butt connector (at least 25x)
-Repaired heater fuse thermal damage and reconnected factory wiring
-Added relay for switched power for all aftermarket devices on it's own circuit
-Integrated trailer brake controller.
-Added switched trailer charge circuit
-Integrated radio wiring
-Added 10ga wire to power heater/AC system in future (to bypass factory power)
-Added theft deterrent circuit to prevent under-hood and under-dash hot-wire.
-rewired non-fused brake warning circuit as a - input to new cluster (won't catch on fire)
-Added fuel pump circuit
-Integrated all wiring into factory firewall plugs so no wires on outside of firewall.
-Converted fuel level circuit to differential
-Removed all unused wiring (old gauges and so on)
-Repurposed ammeter wires into tack and a/c controls
-Support for 3G alternator, EFI, MSD, etc.
-Provisions for adding more aftermarket equipment in future
I used all waterproof/heat shrink crimp connections, like factory, no solder. Wrap is non adhesive vinyl, like factory, removable/re-workable. New connectors are weather pack
I studied the factory schematic to consider the different power domains and fusing. Many functions do not have any fusing, for example;
Ignition
head, turn & park lights
charging
gauges
wipers
No fuse to ignition switch, light switch, or anything on crank/run. That is a lot of unprotected wiring going through firewall multiple times.
In today's vehicles, pretty much everything is protected including critical systems like ECU and ignition. I don't like the idea if a non-fused high current power entering passenger compartment with no way to shut off/isolate, so plan to add a 50A thermal breaker on the factory power wire. Other circuits will get fused in the box I added, except high power audio.
The MDS box will not get a fuse. Why? Because they said so without reason? No, because I researched until l understood and made my own decision. You can fuse and many have.
The reason is related to the 'captive discharge' topology. The main capacitor that stores all spark energy and drives coil is charged to 550V, it discharges through the main red power wire on shut down, as other side is common gnd. So 550V dead short into battery, very high current but for short time.
Got the harness installed. Only the high power main speaker wiring to doors is outside of main harness. It comes from audio amp behind seat so didn't make sense to integrate.
But instead of working on the rest of wiring to get it running, I focused on the most critical system, the stereo. Temporarily hooked up the amp power and the others to make it all work.
It occurred to me that this vehicle had lost it's soul (well, brain, heart, motor, everything) and had not had the key put into ignition for over a year. So it was a satisfying milestone to get audio system working. Tested with some AC/DC, it's brutally loud, as it should be.
I also made significant improvements to high current grounds including the cab, so the amp's power supply isn't collapsing on each bass note. Fiddled with tuning until I was half deaf and beer was empty. Made some motor noises behind the wheel dreaming of the day when it moves on it's own
:)
So if the new motor spins a bearing, flattens the cam or trans won't move, at least the stereo works.
I'll bet it's flawless. 
