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Hi there! You should take it to a parts store and have them retest the alternator.It has to be putting out at least 14.5 volts to be good.You either got a bad alternator or you have bad wiring.
If you have used an aftermarket alternator there is a good chance it is not charging to ford specs.It may be charging at 13.2 volts and that just isn't enough.
Hope this helps!!