It is an incredibly mild tune. I only gained about 10hp on the dyno from it, and it is specific to 93 octane, the only grade I've ran in the 2 years of ownership. The tune is programmed onto a handheld device with the option of returning the car back to stock (for emissions), and the same problem exists when I switch off the tune.
I just checked my own 96 Cobra and #6 and #3 are handled by the passenger's side coil pack. I have no idea what the signs of a coil pack being bad are, but maybe that coil pack is shot? Have you ever replace the coil packs before?