Geez...what a journey.
My replica has some unterminated wires. Fortunately I have had very little electrical work to do, but just like winter, I know it's coming.
If I do it, though, I will map the electrical devices and have a custom loom made...strip the entire other loom and go all new. I see from your photos that the loom covers can hide problems as well as they can protect the wires inside....
I usually put mine on jackstands for a few months in January, this year it will be to get the exhaust system removed, the sidepipes chromed, and get the headers wrapped. I have no doubt that someday it will be to deal with issues such as you are experiencing.
Cheers for tackling this yourself!!!
Dugly