I just got over a problem like this. I ended up rewiring the MSD and made a floating ground for everything else going directly to the battery.
I just got my box back from MSD yesterday. I ran 0/1 gauge for the hot and grounds for the battery and wired the MSD directly to the battery by itself on the sideposts of my battery. I also shielded the trigger wire like stated above. With the combination of it all the miss went away. 8)