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Phil,
I would agree with Dan, and the others in that you should check the wires, cap and I would also suggest the spark plugs. Dan is probably correct in that some of the time the other cylinders must be firing, the engine would not run on just 2 opposing cylinders very well. It wold sound like my fathers old 2 cylinder John Deere tractor, chug, chug, chug, chug. What may be happening now is that since there have been multiple attempts to start then engine with little or no electrical output to the spark plugs, most of the spark plugs are probably fouled. Get a new set of plugs and try them as well. Also, there is a gap between the rotor and contacts for the spark to jump across. Maybe the cap is bad in that the contacts for the most part are recessed too far? Can you take a micrometer and measure the distance from opposing contacts and see if there is a difference? If the gap gets too far the spark will be weaker and possibly non-existent.
this is a baffling problem, there are very few scenarios that would result in only 2 cylinders firing, and even those situations are basically ruled out. If the cap were out of round, you might get a situation where only the 2 contacts that were opposite each other and closest to the rotor would be the only ones able to get spark, but your 2 contact points are right next to each other. The only way that the coil would be implicated is if it was sending weak charge to all cylinders, which is not your case (unless all of the plugs are getting fouled and these are just the last 2). A bad rotor would not be bad on only 6 of 8 contacts.
I just am not knowledgeable enough about computers to know if the programming in the MSD could be off and only allowing spark to go to 2 cylinders, but that does not seem likely.
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