Make sure that the pickup wires that run from the crank trigger to the MSD box are run seperatly from the other wires.
I had the wires run together for years with the MSD distributor setup, with no problems. I put the crank trigger on the boat and started it up and timed it at the house.....no problems ran great. Got to the lake and it fired right up, loaded up gear and family in the boat (still running good) hit the buoys and started to take off and it wouldnt run. So I shut it off and checked for a loose connections everything seemed okay. So I started it back up sounded good started to go and it wouldn't run.
Believe it or not when the one wire alternator started making current it messed up the signal, keep in mind that it ran this way for several years with the distributor and never had a problem.