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Truck runs now with the battery disconnected.

That's a dandy way to burn the alternator out.

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Wire going to the batter from the alt is still really hot.

From the rest of your description, I suspect your battery was very dead, and may well have a dying cell. That means the alternator had/has to work very hard to charge it (hence the heat), and that it doesn't want to take the charge (which is why it took so long to get charged up).

'97 T-100 SR5
'86 Toyota's, the variety pack (all gone)