67 Barracuda Heavy Electric Load

Pictures in post #12 show a relay for the fan so that load is not going through the stock wiring to run the fan. Post#31 shows a new reproduction M&H wiring harness at the bulkhead connector. (OP - M&H sells mostly reproduction stock harnesses but do offer an upgrade to the later transistorized voltage regulator which you have, and for factory electronic ignition - IMHO M&H is the best).

I see no indication that the ammeter has been converted to a Voltmeter, and the pictures of the gauge (post #14) seem to show the system charging before the fan and headlights are turned on (as desired) and then discharging when the headlights and fan are on ( as pointed out in post#22 by cosig). This results in the battery slowly draining down the more it runs. OP - when you start the engine with no accessories on, does the ALT needle pull toward the C (charge) and then slowly recover to just to the right of the middle mark slightly toward C? If so it should be connected as stock as an ammeter. If when first started the needle pulls toward D and then moves to the right, that would indicate the conversion to voltmeter - battery drawn down and then charged back up. Any chance the OP could film the gauge while starting the car and letting it run for a few minutes and post that?

Are the headlights something aftermarket that is pulling a big load through the regular headlight circuit in the stock wiring? If aftermarket are they, too, wired through a relay?

In any case I think the OP is headed in the right direction getting the alternator output tested and getting the battery tested, as a next step. I would bet the "high output alternator" is the factory AC alternator (though it has a single pulley), so 46 vs. 37 amp.

Final suggestion to the OP - I don't know why you are set on using the electric fan, but if it were my car I'd pitch it and go back to a solidly dependable factory fan with a clutch and a factory shroud. I know I will hear lots of blowback, but IMHO electric fans are great for a race car where every bit of parasitic horsepower loss is critical, but for a car you want to drive, not so much.