[FED 387]

1-some Mallory coils are not compatabile with MSD boxes
2-twist your pick up wires to avoid picking up RF signals in the area
3-get a shielded pick up
4-check for proper air gap on sensor to trigger wheel
5-check spark plug gap
6-check for a bad spark plug
7-check points gap in distributor if using points/check the points wire in the dist- shield it
8-double check MSD wiring make sure you do not have a wire incorrectly installed
9-check battery voltage
10-check all grounds
11-check spark plug wires for break/burns/loose terminals
these are things I would look at and not necessarily in this order either
seems like you checked all the mechanical possibilities so it might be electrical , not knowing what your setup is its hard for any of us to pinpoint what might be causing the misfire