I didn't read the entire thread, so don't know what all you have done. Nor, do I know if any of the other experienced electric guys on here have answered any of your questions. However, the fact that you haven't found the problem indicates that maybe the electric nuts have yet to respond.
Maybe, if you could summarize where you are at, one of us can respond. not enough time to read the whole thing.
As far as the harness check, unplug and untie the harness from the hood and front frame, release the fold over clamps under the engine, tie a string to the end and pull the entire harness out from under the engine. This allows you to inspect carefully. The string is for pulling it back into place.