Got to spend another hour or so today working on the project.
Mostly, I just got the batteries out and removed the "bolt-together" battery frame.
I guess a lot of this is all just to get me back into the mind-set of motorcycle design, so I can do it right this time.
When I mentioned to someone else today that I need to rebuild the wire harness, it came up to perhaps transfer the dimensions of the cycle down onto a sheet of plywood. Then run some screws or nails into the plywood and build the wire harness on there.
When finished, just take the whole thing off and zip-tie it to the motorcycle.
Vwalla! Finished wire harness.