A one wire alternator jumpered directly to the battery should have nothing to do with the rest of the wiring
You have disconnected/ cut/ removed something.
You need a good wiring diagram, and see what you cut.
You should have been able to disconnect the stock regulator and just tape off the IGN terminal wire to the regulator. The diagrams below show that the regulator was originally fed split off from the "dark blue" (ignition run feed) going to the ballast. You should still have the one connected that goes to the bulkhead connector
http://www.mymopar.com/downloads/1964/64DartA.jpg
http://www.mymopar.com/downloads/1964/64DartB.jpg
