X2!!! ^^^What he said^^^ An alternator is not a battery charging device. It is a battery maintaining device.
You COULD have a totally shorted battery or something that is preventing the alternator from charging them. Before you jump in and change the alternator, try charging BOTH batteries. At no load, about 3 hours after charging, they should read about 12.7V. Anything less is an indication of a weak battery. A battery charge of 11.4V is a totally dead one.
When a battery gets pulled down like yours were, it is not uncommon for the battery to be bad too, in addition to a possible alternator failure. (Aren't vehicles fun?)
- Jack
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