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depending on how the wires are swapped around, yes. if you swapped the wires around so that one coil fired both plugs on a cylinder, then problems can start popping up, since instead of having two different coils providing a strong + waste spark, you'll have the coil alternating between firing two strong plugs and two waste plugs, which will certainly show you if a coil is weak, since it will do just fine for the waste events but fall short for the strong events.
Ford set it up in what i would consider an optimal arrangement on all fronts. i don't see any possible advantages to firing it the way some have suggested in the past.
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