The V-6 cars spin the alternator at very high rpms, and it is a surprisingly powerful unit at 130 amps. By comparison, a 1988 Grand Marquis with full power options and automatic load leveling utilized a 100 amp unit.
Most commonly a bad ground from the battery to the top of the engine. Some models from 96 and 97 had problems with the insulation on the wiring deteriorating & falling away causing short circuits.
Many aftermarket alternators are not built/rebuilt to the specifications required for the Contour/Mystique/Cougar and you may go through several before finding one worthy of the task. Try a different brand.
Update: I've concluded that MotorCraft alternators are the best option here. They're pricey, but doing this job only once is worth the extra cabbage.
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