The low amperage may be simply because you are trying to charge a fully charged battery, or it may be that for some reason the alternator voltage never rises far enough for the conditions under which you are testing. Also, saying it spins fast means nothing. You need to know the exact rpm under test. You say it stops when shorted. That's good, but again provides no information. One thing you could do would be to replace the battery by a small (high wattage resistor) say 1 to 5 ohms, something that keeps the mill turning and then measure the current. It'd be a rough indicator of whether you have some wiring problem.
