Hi Brendon, actually the 99 and up Mustang's have been giving me fits
There is something going on hardware wise. At first we thought it was due to the PCB board being thinner, but that's not the case.
Once we get it figured out then you will be correct that the same Tuner will work on either vehicle, no changes other than the software will be different because one is EEC-IV and the other is EEC-V.
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Raymond,
Performance Specialties