These are all good points and many of which I've already considered and put into action. First, the wiring harness is from American Autowire and thankfully not only is every wire color coded, they have what the wire is for printed along the length of the wire.
Secondly, at the moment I'm using loose zip ties and rare earth magnets with zip tie loops built in (see photo) . I keep the zip ties loosely connected so that I can route (and re-route) wires as I change my mind about location and routing.
My plan is to finalize the routing of every wire to its ultimate location via the bundles I've previously outlined on each side of the truck engine bay and to the rear of the truck. Then I will pull each section back, one by one, and insert all the wires for that bundle into split side wiring loom, then pull back to its location/route.
The issue still is that the two routes are mid way down from the top of the firewall and the hard plastic firewall cover is going to create an issue if I leave the bundled wires behind it, although only for several inches from the top of the dash to where the access holes are. What seems to be suggested here is that I have those wire loom bundles on top of the firewall cover. I'm going to have to experiment with that method/look to see how it looks.