How Significant Are The Differences Between Pertronix Versions?

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I have the Ignitor I. It's basic and pretty much just replaces a contact set to trigger the coil. It can be used with or without an ignition controller, like an MSD for multiple spark.

From what I have heard, stay away from the Ignitor II.

The Ignitor III is a more sophisticated version that contains a programmable rev limiter and some other functions. I have not seen anything bad about it in print, but would think it would be redundant when installed with an ignition controller.

Another option you did not mention is the OE Ford DurasparkII unit which is also a decent electronic ignition system.