It's been a while since I've dealt with this, and I don't remember the years invoved, but on older Mustangs, disconnecting the harness to the instrument panel opens the circuit between the alternator and the battery, and essentially makes your alternator useless. Don't replace the alternator until you've reinstalled the instrument panel and seen if that fixes it. If it doesn't, then your alternator will need to be replaced. I don't think you'll have to worry about it, though, just put the dash back together.
Take care,
~Chris
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