Alternator and Voltage Regulator Questions

What was the outcome of all this? I have basically an identical problem.

Alternator read low in car; I ordered new one, it didn't charge either. Thought I'd get them tested before I ordered a new VR (the current one can't be more than a few years old). Autozone gave me the green light on both alternators, Advance auto says the old one is bad (haven't had them check the new one yet).

Thought I'd do my own electrical testing and half-assed it, causing a massive short to ground, absolutely frying the fusible link and the bulkhead connector. I'm going to start by rewiring the charging circuit directly to the battery, but I don't think that's going to solve my VR troubles.