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You are going to have to check to verify this on an 07(someone more knowlegeable please chime in) but on our 01 the PCM grounds/fields the alternator only after the 2 minute timer to energize the glow plug relay has elapsed and, I believe, other input info doesn't require it to turn on the air heater relay. Is your Wait To Start light going out? You'll need to check voltage at the relay to make sure the solenoid isn't staying energized. If it is the PCM won't field the alternator. Also, have you had the batteries load tested? Have you jumped it off recently? Anything unusual happen to it? Scroll down and find my post A Word of Caution for some electrical system pointers. Take your time, don't throw parts at it, you have to find the actual problem first. Your owners manual will show you the location and task of relays and fuses. Sometimes just swapping them will solve a problem.
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