-Mach 1 motor isn't forged like the Cobra motor to handle the boost from the Supercharger, also the Cobras block is made from Iron (i think) vs aluminum like the Mach 1s block.
-Cobra also has a 6 spd tranny vs 5 spd man. or 4 spd auto for the Mach.
-Interiors differ some.
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suspension (previously stated)