You need to check electrical connections. To begin with make sure that the connector on the back of the alternator is properly seated. Check for loose grounds and loose battery cables. It also wouldn't hurt to pull the voltage regulator from the alternator and make sure that there is still some brush length.

It also wouldn't hurt to do a voltage drop test between the alternator and battery. That would show up any bad or flaky connections.

If the problem comes back and stays a problem instead of fixing itself, check the battery voltage at a fast idle to see if the battery is charging, then go from there.

Good luck,