jfralick,
You sure have covered all the bases. I have no idea where this clue leads, but the back three cylinders...4,5,6 are smack dab between the problematic cylinders if you run the firing order.
If it isn't something mechanical then it still looks like a coil/voltage problem.
If you have a ballast resistor, your rig must be 12 volts! You don't have a internally resisted coil TOO by any chance?
What exactly happens when you hook up all the wires and run the engine. Does it run poorly, snort and backfire or just act like it misses.
If you can replicate the problem, maybe you can sneak up on it by changing only one variable at a time. This should allow you to shed light on which system is a fault.
It almost seems like the coil has only enough dwell time to saturate for every other cylinder..5,6 and 4.
As HevyHauler said...this is a real toughie! :confused:
Stuart