Here's some basic advice as far as electrical:
Lay out the harness on the floor and spread it all out. Use your wiring diagrams and schematics to figure out what each and every single connector is and does. Label them. Do one harness at a time and have a second set of eyes with you, mislabeling something costs a lot of time and headaches later down the road. Ask me how I know.
Label the Jeep and Ford harnesses with different color tape. I used green painters tape for the Jeep, and orange painters tape for the Ford. This way when there's a thosand connectors flying around the engine bay, you can kind of visually get a snapshot of where everything is falling in place.
As you're going through the harnesses clip off things you aren't going to use and yank that from the main harness (air conditioning, smog pump, etc). Size matters here, the smaller and more flexible the large looms are without all the unnecessary wires, the easier it is to route them around the engine bay.
Start with partial harnesses that connect to larger bulkheads. For example; start with the fuel injectors, tps, egr, and coolant temp sensors, these are all found on the same smaller harness that connects into a larger one. Keep doing this for all the smaller independant systems until they are done and ready to plug into the main.
Don't even begin wiring until every bolt on the top end is in, gasketed, and torqued to spec. The last thing you want to do is have to pull your upper intake maniold after there's miles of wires in the way.
After the engine is done as far as you can go, get to work on the chassis harness. Get all the basic wiring done and all the connectors in and set before you touch a pair of wire strippers. When you're absolutely positive that there is nothing else you can do without hacking in, only then begin to make things like the alternator tie into the body harness. I'm still working on this myself, because I'm thinking I'll have to use an inline fuse and possibly resistors to feed the correct voltage to the Jeep body harness which in turn feeds power to and communicates with the Ford engine harness. This is the point where things get really sticky and your brain begins to sizzle like bacon in a pan. Math hurts.
Most important:: USE THE CORRECT TOOLS AND SUPPLIES. GET PROPER WIRE STRIPPERS, SOLDER, HEAT SHRINK WRAP, A MULTIMETER, AND USE DIALECTRIC GREASE ON EVERY CONNECTOR. Seriously, don't half-a** this. You'll pay for it later. I personally am making my own schematic on draftboard paper so that I have detailed records of what goes where and does what, complete with wire color, resistors, voltage, etc. This is so much better down the line when I want to service or change something and I'm not chasing through my previous work and a bung of factory manuals, scratching my head and wondering "what the hell was I thinking when I ran these wires like this?"
Good luck. Catch up so that we can help eachother