Your initial post didn't mention jumping the car, only re-charging. However since PCM is still under warranty you should fight the charges, although you may have to pay dealer first and fight Ford later.
Make sure you recover old PCM since there is a chance dealer is wrong and that it's only key programming problem and not fried PCM.
98 Mystique LS v6 atx 110,000km
97 Contour LX v6 atx 125,000km
stock CD on LS, cass on LX
spoiler, tinted windows on LS only
4 wheel discs on LX only
All other available options on both
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