No more than 12.5 charging-Has to be VR problem?

Vreg regulates the drop from IGN1 at the Vreg wire to its case. It tries to keep that at ~14 V. If you measure close to that, the Vreg is doing its job. You then need to find where the voltage drops are from its IGN1 to your voltmeter and its case to your voltmeter gnd.

Usually when there are voltage drops, Vreg overcharges the battery, so your results are a mystery. It sounds like your alternator is not outputting current, since sounds like your measured voltage drops when the engine is running. Does your dash ammeter work?

I have a clamp-on DC ammeter I use in testing to measure alternator output. Before that, I would wire in a series 100A ammeter for testing, i.e. in my cars w/o a factory ammeter. If not hard-core, buy a cheap cigarette lighter voltmeter (Harbor Freight, Amazon). In all my cars, I see >13.5 V when running, if the alternator works.