Have you tried the old analog style MSD 6AL on it? I had all kinds of misfiring issues w/ the MSD Digital 6...not the newer digital 6AL like you have. Sent it back, got a new one, same thing. Had it mounted under the dash where my old style 6AL had been. Ended up getting my money back and have been running the old school 6AL ever since w/o any problems. Those digital boxes are extremely sensitive. 
CHIP
'70 hemicuda, 575" Hemi, 727, Dana 60
'69 road runner, 440-6, 4 speed, Dana 60
'71 Demon 340, no drivetrain, on blocks behind the barn
'73 Chrysler New Yorker, 440, 727, 8.75
'90 Chevy 454SS Silverado, 476" BBC, TH400, 14 bolt
'06 GMC 2500HD LBZ Duramax
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