If it is a stock 49, you shouldn't have an alternator.
Can you post up some pictures of what you have? I have a few suspicions, but I don't want to muddy the water with potential misinformation.
Or if you have the part number of the one you just got from the store, that would help.
One last thing to try: I suspect you are measuring the battery voltage with the engine idling. Most alternators need to be spinning at a minimum rpm to charge.
Try reving the engine up to 1,000rpm or so and check the battery voltage then.
