Not sure if this is relevent - the shop that rebuilds my alternators and starters told me you should never use the alternator to recharge a low or "bad" battery because it could fry a diode or two. That's what happened to me before I had an alternator rebuilt.
The shop owner said to fully charge the battery before running the engine with the rebuild - and make sure the battery is good (holds a charge overnight, or a couple of days).
Hope this helps.
