There is a fusible link between the alternator and the starter. It charges the battery through that connection. If it was not correctly reattached or has been blown (like a fuse), then the battery will not get charged.
When there were wires smoking during a jump start, that was a sign right there of bad things. It could have been just the starter that died, but an inspection of the wires and cables would be a good thing, just to be sure you don't catch fire out of nowhere.
I'm in favor of having that alternator tested, even though it was just purchased. Like @repairman54 said, DOA is not unheard of.
When there were wires smoking during a jump start, that was a sign right there of bad things. It could have been just the starter that died, but an inspection of the wires and cables would be a good thing, just to be sure you don't catch fire out of nowhere.
I'm in favor of having that alternator tested, even though it was just purchased. Like @repairman54 said, DOA is not unheard of.