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It sounds like you have a intermittent wiring problem on the red wire going between the pcm and the fuse. You will need to monitor voltage on this wire at the pcm when problem happens and if it looses voltage then do the same thing at the fuse, if it does not loose voltage then replacethe wire between the two points or check connector/pin conditions. The alternator has a internal voltage regulator and if that was the problem it would not charge like it should. Let me know if you have questions, thanks.