Voltage drop issue- where to go from here

I removed a voltage regulator wiring harness from a mid 70's Dodge P/U, had three wires on it, one to switched ignition, then the other two to the alternator (black one to lower post (the one that's currently jumpered to ground with my current VR) and a red one to the upper post (which is currently connected to the green wire on the single pin VR I am using currently)
My switched ignition line I ran to the switched source that the old Voltage regulator was ran to, IE the lower pin on the ballast resistor.

Oh and FYI- I don't have a bulkhead connector on my vehicle. It was removed and bypassed prior to my purchase of the vehicle, and was covered with a large rubber sheet with holes drilled in it to let the wiring pass through (actually a pretty ingenious way of sealing that hole... pretty water resistant lol)

Now- Redfish, your comment about the relays... Where would I install said relays, where would I run them too, and how would I wire them? Any suggestions? PM me with some details.. Im not against using relays, not in the least (I love relays actually... they help keep the magic smoke inside the wiring instead of escaping to the outside lol) but I still want to get to the source of my issue.