If the alternator tested good when it was out of the car, then I would say there is probably a bad connection somewhere.
Perhaps a corroded connection to the voltage regulator (built into the alternator - should be a 3 wire plug on the alternator).
Here's how you can test the output of a 12v alternator yourself, with a multimeter:
With the alternator and battery installed and hooked up;
Engine Off:
You should be able to test the voltage at the battery posts and get somewhere around 12v.
Engine Running:
If you test the voltage at the battery posts, you should get somewhere around 14.5v (also it should be 0.5 to 1 volt higher
if you turn on the headlights, than with them off).
You can also test the voltage from the alternator connection to the engine or body (or alternator case), to determine if
there is a bad connection between the alternator and the battery.
I was gonna check mine and tell you how to test the wires to the regulator, but when I went to test stuff I discovered that
my alternator isn't working either. :/