Something is still strange. You are still getting non consistant results in my opinion. If the meter is a recent aquisition take it back if you can. Barring that borrow one.
I very much doubt the wiring harness has some open leads. Anything is possible yet..... You will find a normal working meter to be much nicer to use. At this point I would not trust that meter you have. Most meter problems are constants but your meter may be throwing a few curves in for good measure. Since you have alligator clips etc try putting a 12 volt light bulb between the positive terminal of the battery and each contact in the plug. If it lights the plug for most practical purposes is probably useable. If it does not light you have an open plug most likely. I suspect your results might be different than your meters. Sorry to see you having so much trouble.