6. Cylinder duster is now a 340 ignition issues wants to start when you let up on the key

Yes.
Trying to figure out what he's finding on the car.

It seems like it may have the '65 Amp' alternator wiring.
A1F and R6E through a grommet on the firewall.

So according to the connector drawing you just posted, then A1D is capped or removed, but R6D probably was left in place.