I don't think there is anything wrong with your harness.
Everything was working fine until your battery light came on.
Your car runs fine until you connect the new alternator, but your old alternator doesn't blow the fuse.
Having zero ohms from the positive post on your alternator to the metal case is wrong.
If there was something wrong with your harness, it would blow the fuse with the alternator disconnected or with your old alternator connected.
Check the resistance of the donor car alternator between the positive post and the metal case.
It was and probably still is working.
I'm almost positive that all you need is the donor alternator.
On my car the battery light comes on when the voltage is too high or too low.
When an alternator gets old, the brushes inside wear out and no longer make contact then the output stops.
Your brushes may be wearing out and they are only losing contact at higher rpms.
So I replaced the harness unfortunately the guy didn’t have a tester on him and neither did I also my old alternator blew the fuse in the first place but I went through an disconnect and checked every wire in the harness and it’s all fine so I think you are right the only thing that could still cuase this to happen would be the alternator so I will talk with home tomorrow and see if I can get it it looked pretty corroded but still usable so I will see if I can swing by and test it or get him to test it for me