Your "endless crank" then start when you release the key, is indicative of no "crank voltage" to your MSD box. Could be a starter relay sort of thing.
Fords (and others perhaps) supply 12V to the coil when "cranking", then once the engine fires, the operator lets off on the key and it returns to the "run" position, and the ignition system now provides a reduced voltage amount (6-9V) to the coil for normal operation (via a resistor wire from the ignition switch to the coil, or an external resistor of sorts). With the aftermarket setup, I suspect it operates in a similar manner, but you perhaps inadvertently removed one too many wires!
You are correct in removing the fuel pump wiring, electric choke, the subwoofer wiring, alarm, fog lamps from the coil hot lead.....!
If you have a Mangusta, it's 12V cranking and 12V run.....but you must have a coil that is made to operate that way....some old Chevys were like that.
You may want to check the coil to see if it is now getting 12V at cranking....
The fact that it is running at all says your coil and plug wires are "OK". Misfiring under load is something that could be attributable to a bad coil wire or one or two spark plug wires....check for header burns!
I suspect your butchered wiring to be the problem. I've heard this symptom before on other members cars, and I think even my car too, when I first got it....crank like the dickens, and as soon as you let off the switch, VROOM! Now, I barely turn the engine over one turn and it is running.
I'm an advocate of Ford Duraspark II systems....simple, easy to troubleshoot, and you can steal parts off of almost any Ford product made from the 70's to early 90's to get you down the road!!! A little harder to get aftermarket parts out in the weeds....
Keep on with it, you'll nail it!
Steve