I've been sorting out the wiring on my '53 4104 now for a bit. Generally it's gone well but slowly. My 1st inclination to rip it all out and start new still might have been faster, but I have enjoyed working through the wiring diagrams and getting to know my bus better.
1. One of the things that has always bugged me about the bus was a constant drain on the batteries....I'm not sure how much but it would always have a load on the battery....turns out the old relays that I kind of like because they are so rugged and tunable also leak current.

I was working on the horn relay when I discovered there was + current "B" terminal when the points were open....this makes no sense really, but I guess internal corrosion is causing some part of the relay to short. Only 2 volts were sneaking through so I guess I could use it as some kind of resistor. Anyhow I replaced it with a little cube relay, and I guess there will be a few more to change along the way. I've got tons of cube relays pulled off of transits headed for the great bus yard in the sky.
2. The other thing I have learnt is that fixing stuff can really make things worse. Case in point , when I rebuilt the rear control panel (the one that allows you to turn on the engine from the engine bay) I let loose a sackful of snakes). PO or more likely POs have wired around all the shutdown systems over the years (I would have down the same), but when I "fixed" the rear control things got wonky all over the place. All of a sudden the charging indicator tell tale on the dash would turn on when I turned on the marker lights. Took awhile for me to figure that one out as the marker light issue turned up 3 months after I had "fixed" the control panel.
3. remove the front seat when working on control panel. Fixing old wiring is hard enough, pull the seat and get a nice cushion to sit on, oh and absolutely use a drill driven socket to screw and unscrew the junction post nuts.
Anyhow just thought I would pass this on in case anyone needs the info.