I forgot you had a modified alternator... So at high idle >1K or so, you're seeing at least 13.5 V and the battery charges even with all the electrical loads on? If that's the case, you need to raise the RPMs of the alternator at idle -- an overdrive alternator pulley would do this. Don't know where you can get one of those though. Underdrive pulleys can be had, but I don't know anyone that makes an overdrive pulley for an FC alternator.
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