I'm not a mechanic Stephan, so I could be wrong, but I would think that your alternator output would be a good place to look. At high revs, you could be looking problems concerning the output to the battery being something that the computer doesn't expect (i.e. the charge being too high or too low) That particular problem could range anywhere from a small open or short in the circuit to a problem with the alternator brought on by high revs or vibration... or maybe even the belt (does it seem to slip at all?)
Just some guesses...
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98 GT
Dyno-Max cat-back exhaust, 3.73 gears, Steeda shifter, Ford Motorsport Underdrive pullies, 87mm MAF and Roush cold air kit...
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