The van's engine bay harness/battery junction box is now nearly finished. All that isn't needed has been removed and the new circuits have been neatly fit into the fuse panel. I have a couple relay circuits left to finish up but that will only take a few minutes now that everything is wide open. My goal of no butt connectors is still in play since I was able to re-purpose a few wires with the correct terminals already on them. The harness has been reconfigured a bit to account for different locations of things between the 5.4L and the Cummins too. All of that was pretty easy when the harness is all stripped down bare.
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This is admittedly a ton of work but I believe going to these lengths is necessary for a project like this. And now that I've done both the engine side and van side harnesses, all the while taking notes and making up my own pin-out charts, doing this again won't be too bad.