First off, disconnecting athe battery while the engine is running is the quickest way to damage an alternator. Unlike the old DC generators, the alternator needs the battery in circuit to protect it against voltage runaway.
If the alternator has been bench-tested and seems to be functional, I would start by verifying the related vehicle circuits. Witch a DC voltmeter, start out by measuring the voltage at the alternator's output terminal, the heavy black/orange wire. It should be full battery voltage. If it is anything less than battery voltage, you must determine why. Some things to look at are the gray 12-gauge fusible links A & B, and the various splices and connections in the circuit (see diagram below).
Next, disconnect the voltage regultor harness plug from the alternator and check the voltage at the wiring harness regulator plug's "A" terminal connector - the yellow/white wire. It too should be full battery voltage. If it is anything less than full battery voltage, you must determine why. In this case, look at the 20-amp ALT fuse in the battery junction box, and at the various splices and connectors in that circuit.
Then, turn the key switch to its "RUN" position and measure the voltage
at the wiring harness regulator plug's "I" terminal connector - the light green/red wire. It should be somewhere between 8 and 12 volts. If there is no voltage present, check Fuse 5 (15 amps) in the main fuse panel and the various connections in that circuit.
The final test is to measure the voltage between the batterty positive terminal and the alternator housing or frame. If it is anything less than full battery voltage, check the alternator mounting.
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