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Quite some time back I installed a dual Ford Contour fan. I have the 130 amp 3g alternator, and an MSD 6a ignition. MSD is wired to batt +, and the fan to the solenoid. When the fan kicks in the ignition (engine) stumbles.
I'd like to fix that problem. I believe the dual fans pull about 25 amps as both kick in. That's 25 amps total. I'd sure like some ideas about how to remedy the problem.
Not ever having run a MSD, anything I say is entirely speculative. I do know they are funny about outside influences. One of the reasons they advise running power directly to battery. A simple thing like running the MSD and fan power wires loomed together could cause an induction problem between the two when the fans cut on. I have read of induction being a factor especially in the triggering circuit. Take this with a grain of salt.
If the ignition module is to blame, then it sounds like inrush current from the fans is pulling the supply to the module low briefly, which it sounds like you're suspecting anyway. You might be able to catch that on a multimeter if it's quick enough.
When you say the MSD box is tied to battery positive, do you mean it's literally somehow tied to the positive battery post? I don't know if the difference would be enough to cause the issue you're seeing, but I wouldn't recommend tying a load here, one of the reasons being that the positive battery post is not at the exact same potential as the alternator's sense point (the A terminal). If you don't have it tied to the battery post and you just meant "batt +" to mean 12 volts, then nevermind.
An internally-regulated alternator like the 3G would hopefully be able to respond quickly enough to keep the MSD box's supply high enough during an inrush from fans coming on, but if there's any unwated resistance between the 12-volt supply and the box's supply terminal, as well as the box's ground and true ground, then the current pulled by the module when the supply dips may be enough to brown out the MSD box. Check that the wiring to the module is clean, tight, and robust. With the engine running, try measuring the voltage across the box, then across the battery terminals, and make sure there is minimal difference between the two levels.
The only other thing I could suggest would be to add a bulk capacitor next to the supply of the MSD box, similar to what is done for large car audio amplifiers (but those capacitors are not rated for under-hood applications). However, the MSD box should have enough bulk capacitance inside to handle this anyway, so you should not need to do this. That's why I suggest looking for any drop between the supply and the module. It's also possible the alternator is faulty or the alternator's output wire is too thin of a gauge.