i have THE SAME PROBLEM on my car. it started out as the throttle position sensor wire was almost cut through on the wiring harness because i had an SAFC hooked up. i redid the wires, and took out the SAFC. the car used to stutter allt eh way through the power band and now it only stutters if i have the MSD installed. i'm guessing the added voltage from the SAFC is causing the coil to spike (stock coil 170k on it) if i disconnect the MSD it goes away, but it has much less bottom end power without the MSD on it. could i put my 3L coilpack on or will that not comply with the 2.5L wiring harness?
oh yeah and i should add that i run the plug gap with the MSD at 52 thousandths. i ran it at 40 without but i havent changed it lately. i'm going to try new plugs again. my car right now also runs worse after it rains, which makes me think something makes a voltage change somewhere, like a wire is exposed and gets wet or somethign of that sort. any ideas folks?