I feel your pain, I had a '86 Grand Wagoneer that I built a 401 and put the early Holley four barrel digital fuel injection on. Had MSD ignition and a Ford E-core coil. It was my daily driver for 10 years.
When I run in to problems like this, I usually go back and check the basics. Does your distributor control the mechanical advance, or is this computer-controlled? A mechanical advance that's hanging up would cause your erratic timing. Have you put a new distributor cap, rotor, wires, and spark plugs in it? Are you sure it starts misfiring, and not just low idle speed from a faulty Idle Air Control motor? Not having eyes and ears on the vehicle sometimes makes it difficult to diagnose. Sensors that are glitching out and sometimes only be caught with the lab scope, not in datastream or with a voltmeter.
I agree completely with setting up a separate set of timing marks where you can view them easily. A temporary set up can be made by bending a piece of coathanger and securing it underneath a timing cover bolt, and then scribing a mark on your harmonic balancer. Bend the wire so that they line up at 0°, and then use your advance timing light to see what the actual running timing is. I have had Fords only run with the base timing plug (called the SPOUT connector) unplugged and that is almost always the ignition module, but again that is on Ford's.
When you have several systems working together, it is more difficult to diagnose than a factory original, but isn't that all part of the fun? You'll get it, just step away when you are frustrated, and follow the symptoms. Remember we're all pulling for you, we're all the this together (Red Green).
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