I fought this same problem with my daughter's 99 F250 last summer, having the alternator rebuilt and buying a new one from NAPA. NAPA's alt test machine showed the fresh rebuild to be bad, so on Monday I took it back to the rebuilder and he tested it proving it would put out 120 amps. He did the tests right in front of me, and laughed when I told him the NAPA alt tester story. He said "sure they want to sell you their $100+ alternators (reman in Mexico)".
With much frustration, and encouragement from the alt rebuild guy, I kept digging until I found the problem in the factory wire harness beneath the batt box on the right side fender. Either batt acid or road salt had gotten into the covered harness and got to the junction where the 2 fusable links, the big alt output wire and the one small wire that feeds back to the alt plug. The small copper wire was down to about 2 small strands and a lot of green copper dust. The voltmeter would read 12 V, but it could not carry enough current to excite the alt. Trimming all wires back to solid copper and soldering them together and taping the heck out of it made everything work correctly. I had nearly pulled the dash wiring apart trying to find the problem there.
Don't trust a good looking wire harness. I spent days trying to find the problem. Alt rebuild guy said Ford PUs have this problem somewhat commonly. An easy test to prove your wire harness is OK is to use a spare 12V headlight bulb with 2 test leads. Hook one lead from bulb to ground, and the other from bulb to the unplugged wire harness side of the alt plug with the ignition switch turned on, engine off. One of the small wires in the plug is switched by the ignition switch, the other one is a back feed from the battery (through the possibly offending wire harness). The headlight bulb limits the current to about 5 amps, so the small gauge wire is not injured. In this test I have described, both small wires (each separately) in that connector should fully light the bulb. If the bulb lights with both wires, the dashboard side of the circuit is OK, and the wire harness going to the fusable link is OK. If I had known of this test, I would have saved a lot of time and $$$.
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