At the wires leaving from the battery - you have a short in one of them, their insulation is compromised.
But you should also check the alternator on its own - it might have also been shorted.
Use an ohmmeter for testing.
Look at heavier items, like alternator. by pulling the fuses and relays you have eliminated anything downstream from those items, just keep going. Diodes in the alternator are a prime suspect. Pull the wires to the alternator and test again...
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When the alternator is disconnected from the battery I show a drain when the battery junction box is supplied with power, however, when the alternator is supplied with power and not the BJB there is a drain. I have isolated this drain to the small wire from the battery which connects to the alternator via the plug,( the wire to the PCM when connecter does not induce a drain.) Where i am confused is, is the problem in the alternator or the some where else? How can I have a drain with all the fuses and relays pulled?
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