67 Barracuda Heavy Electric Load

OP - Does the wiring for the regulator (wires to triangular plug) appear to be a part of the M&H harness (wires coming out of the wrapped harness)?

If so, again, I would bet that the upgrade to the later voltage regulator was done by having M&H build it that way, which is an option that they offer on their under hood harnesses for earlier cars, as opposed to a PO wiring it in by the seat of their pants. That of course does not mean the the VR is operating correctly. And does not mean that the fan harness with relay is not incorrectly wired. If the OP disconnected the fan and started the motor cold, could he run it for long enough to see if the electrical issue goes away? The water pump is still driven by a fan belt.