Yes, there is different (magnetic--NOT electrical) polarity--that's why one coil set is wound backwards from the others.
The ROTATION of the distributor means nothing. That is why Oldsmobile can use either coil set and it is correct--depending on the location of the starter.
It is also why Buick (distributor rotates clockwise) and "most" Oldsmobiles (distributor rotates counter clockwise) use the same coil set--and that coil set has the same polarity as Pontiac (distributor rotates counter clockwise) although Pontiac uses longer leads on the pickup coil, and so it gets it's own color code.
As best as I can figure, the module triggers off of a pickup coil waveform when that waveform starts to go negative. The magnetic polarity of the pickup coil is chosen so that interference radiating from the starter/starter cable/alternator will cause a positive spike that the module is able to ignore. So, yes, polarity of the coils is important--but NOT because of the direction of distributor rotation. I do not know why the ignition coil is also magnetically matched to the pickup coil--but it is. That is to say, the car will run with mis-matched components, but it will work BETTER if the pickup coil is matched to the engine family/starter position, and the ignition coil is then matched to the pickup coil.
The "five page" thread you were talking about is an excellent but very long read:
http://216.178.81.108/forums/showthr...&highlight=HEI
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