How many miles are on the car? You may want to yank the IMRCs and clean those out. Youd be surprised how much gunk is built up in those. Do you have any motor mods that you think can cause it? And about the MSD, those dont play very well with the 4.6s & coilpacks. The coilpacks are about the best spark you can get. Just get some 9mm Ford Racing wires and be done with those. You have a gear in it yet?