what serial number series?
I am pretty sure about the only PSBs MCFA has ever put out in relation to the "square" coil was one about the sympathetic vibration between the engine, the frame and the coil bracket which caused the coil bracket to crack and or the switched battery positive wire breaking internal to the insulation (which can be a cause of backfire). For me, pulling on the wire usually shows some point that it stretches, where the insulation is still good but the wire inside is broken, very often in the short bit of wire that runs between the frame and the coil.
Now, that said, how are you watching the spark*? What is the voltage of the battery while cranking? When you tried a new pickup in the distributor, and did you install it correctly using the correct grease? Have you gapped the plugs? (no guessing, it really does make a difference, on this motor especially). Is there ANY side free play in the distributor shaft?
I do admit to always carrying the bit of pre-made wire harness that runs between the coil and the distributor, and sell it along with a tune up.

~ just joking below this point~
* = can you get a video for you-tube of an intern to hold the spark plug wire in one hand and turn the key with his other hand?
~don't try this at home ~