Hy. I have, in my 6 cyl 232 AMC engine, the MSD set up:
-Blaster II coil (45000v)
-MSD 6A box
-MSD 8.5 mm wires
-MSD Billet distributor(8516)
-Spark plugs gapped at .050

...followed the instructions and it works fine. I do not have that problem(continued motor run) but there is a section in my instructions that mentions something like that, in case of a car not turning off when the ign switch is turned off. I did not pay attention to it since it did not happen to me, but I will check into it.
I do not have a HEI system, but I think the MSD 6A box has a diode or something of that sort in the kit(instalation), for the time when what you are experiencing now happens. I think it is due to the system being capacity discharge, more potent and with it's own energy(stored in a capacitor), so the diode(SUPPLIED)has to be installed within the system according to their instructions. Check out the instructions. Also, MSD is good with technical support, I called them to verify the spk plug gap, and also with questions about my MSD distributor( finding the correct dist curve) and they are very helpfull,excelent support. The number is within your instructions.
Give them a call. I will read my instructions about the dieseling/ diode in question.

JaIME.
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232 6cyl*Weber 32/36*6 into 2 headers*MSD distributor*MSD 6A ignition box*MSD spiral ign cables*ACCEL super coil.