Misfire after installing Permatune

I noticed a slight misfire after installing a Permatune in my car occuring at about 5000rpm. The car pulls through it, but it does bug me. Magnecor wires, MSD Blaster 2 coil. Doesn't occur with the stock ignition control unit. Reading the Permatune website, I see that they indicate installing a Permatune will often make existing problems with the stock system more apparent. I also see they offer a complete new harness for the 911SC to deal with this problem, so I'm wondering if it might be the shielded wire from the distributor pickup to the ignition box - any other ideas? I believe all other components are OK, but is there other wiring I should check?