Holy crap, Spaghetti !
There could be all kinds of #$%* wrong with that set up. I'm seeing pieces that are normally isolated, that are not.
Seeing allot of splicing, are all your splices leaded and good, did you shrink tape them and are they going to the right places? The right places would be key.
Are your grounds good? do you have grounds?
Find all effected wires trace them to both ends,see if the connection to it is correct and repaired, run the line with ohm meter check for over all continuity then check the same wires for shorts...
A wiring harness takes up no space, doesn't weigh much, and can be left intact for the re positioning various components simply by extending a wire using the provided factory plugs. And is always the first thing to be massacred when the obvious has been overlooked.
So recheck your wiring plan , redraw and doublecheck what goes where so there is no question about that ,and you don't get confused from back tracking on stock wiring diagrams . It would then be left to the quality of the workmanship and the condition of parts.
You will either find the problem or you won't- you will either use this wiring harness or you won't- you will have the patience and knowledge to repair this harness or you won,t. If you think you won,t , save yourself the irritation get another harness ,don't cut it ,extend it to reach the re positioned components,
insure that it works first, then alter if you must.