65 wiring harness meltdown

I think you mean the small wire on the solenoid, the one on the right side as you face the solenoid? If so, that is the wire that should go to your coil. It should supply +12V directly to the coil, bypassing the pink ballast resistor, while the starter cranks. That should have been a brown wire at one time but its REALLY brown now.

Exactly why that wire would be fried is unclear. Just a theory: possibly dreaded former owner wired in some super-duper low resistance coil and didn't know to disconnect the wire from the solenoid. In that case when the starter was cranking there would be a LOT of current thru the brown wire which it was not meant to carry. Or somehow the wire to the coil was shorted and even more current was going through it. Either way, I doubt there would necessarily be a problem with anything on the driver side of the firewall although it would be a good idea to take a look to be sure. Alternators are pretty sturdy and can melt a lot of small wires with little affect to the alternator. Actually, I would think this wire was fried by some problem unrelated to the alternator.

With a new wiring harness and properly wired ignition you shouldn't have that problem - whatever it was.

Yep, that is the wire. Used to be brown.

Got a new harness yesterday. I ordered one for a 65, but the new harness doesn't have all the same wires as the old. Old has a yellow wire that is connectected to another wire going down towards the frame, and a small red that is connected to the large battery wire terminal on the solonoid. I am going to look for a wiring diagram online because the book I have is a bit vague - no good wire diagrams.
Since I have no way of knowing what the previous owner(s) did I am just going to try to make sure things are correct 1 pc at a time. 1st goal is to make sure the burnt wires are replaced and correct. Makes me unsure if I have the correct new hrness or not though. I'll try to attach a pic of it. ( thanks for the input by the way)

First of all does your car have a Ford ammeter in a '65 GT style instrument panel?

I sense a problem here. Sounds like the 'old' harness you have is for a '66 which all had ammeters; those ammeter wires are yellow and red as you describe. The '65 ammeter was wired differently and I have yet to find a schematic that tells me exactly how. The '65 ammeter was a direct reading ammeter with a current loop on the back with no direct electrical connection of the loop to the meter (its all done magnetically). The '66 and later were shunt wired and had 2 terminals on the back of the ammeter like the other instruments although the ammeter innards were hugely different than the other instruments. As far as I know the '65 loop-thru ammeter is a rare bird that is NLA. The picture you attached seems to not have the yellow and red wires hooked up.

Do you possibly have a '66 ammeter as a replacement ('65s being unavailable)? If so, then what you need is a '66 harness which has the yellow and red wires. Or possibly your old harness was for a '66 and they simply didn't hook up the yellow and red wires for an ammeter that wasn't there.

I will await more details of what you have there.

OK - here goes.
No, there is no ammeter at all that I can see. There is only a ALT light in the gauge cluster. Did have an aftermarket voltmeter wired in though.

I think you are correct about the old harness being wrong. When I disconnected it at the firewall there are 2 more wires on the "old" harness than there are connections coming through the firewall in the plug. In the group that goes to the solonoid is where that yellow wire is. It is plugged in - and it is plugged into another yellow wire that goes down toward the front of the car and goes into a harness there. I looked at a diagram from the Care & Feeding of Ponies blog and it looks like it may go the volt reg (?)

Also looks like there has been some creative splicing in the dash as well. I think I should probably get them correct one pc at a time and then move to the next spot in the line. If I can get this one harness hooked up right then I'll check the other connections under the hood since they are easier to see. Then move inside the car.