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Most parts shops will bench test altenators for free, at least around my neck of the woods they will. Also check the batteries separately. Disconnect both the batteries and check each one by itself. I had one bad battery discharging the other just like you had and if they weren't disconnected the bad battery would test as good.
Once I replaced the batteries I had no more problems for a year and a half then I ran into the same thing you are having. I never figured the problem out as I traded in my 99 on a 2010. Good luck.
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