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The electronics should be powered by the battery, not the alternator. The alternator merely charges the battery, so I'm not sure that a one-wire alt will make much difference. Methinks you are going to need to solve this problem the old fashioned way - eliminate one potential problem at a time. 1) connect a multimeter in series in the MSD hot lead and watch the voltage when the fan goes on and off, 2) same thing on the coil hot lead.
Good luck,
Brian
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