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Quick question, Does the charge indicater light come on when the key is turned on? That goes the Wht/Blk wire at the alternator and is fed by a 15A meter fuse. The Blk/Wht is powered by the 30A fuel injection fuse and the Wht/Grn is powered by the 80A main fuse. You really need to have this charging system tested with a VAT tester to check voltage, peak amperage and the diodes to find out exactly how that alternator is perrforming.. Your shooting blindly here.
Alternator Precautions Mazda 323/MX-3/626/MX-6/Millenia/Protégé 1990-1998
Several precautions must be observed with alternator equipped vehicles to avoid damage to the unit.
Never separate the alternator on an open circuit. Make sure all connections within the circuit are clean and tight.
The rest of the article and precautions can be read here
Here's your schematic but I've already described everything on it.