You would drill a ~1/2" hole on the flat top of the cap between the center post and the #1 post & set the throttle screw at 2000 rpm & connect your timing light to #1 plug wire & point it straight down onto the rotor & see how far away from the underside of the #1 terminal the rotor blade is. If between a stackup of tolerances, your curve(initial & mech) at 2000 plus the vac adv amt the rotor could end up being)at that point) just far enough away that the spark has trouble jumping that distance each & every time & hence the misfire. You could use an old cap if you did not want to drill your MSD cap though the hole is good for letting the ionized air out(which also contributes to misfire for the opposite reason) & a faster check might be to adv your initial 5-7.5 degrees & try it then retard it 5-7.5 degrees & try it one of which will swing the rotor closer to the terminal & help you if rotor phasing(the distance) is the problem here.