First record was MM1300 in the Frank, and possibly in the Destroyer -- though maybe still the Super 70s (which sounds similar in that application).
The unequal coil thing was much later - and pretty evident. You can hear the difference on boots and on the records. Fair Warning...anything with a bar (Franky) has a Telecaster-on-steroids tone, the stuff without a bar (Push Comes To Shove solo, for instance) is '59 Les Paul. Much fatter.
I think this unintentional coil tap thing partially led to the higher gain quest Ed went on.
Now, the original Seth Lover PAFs had pretty random coil windings, especially later as production increased. But nothing RADICALLY different unless there was a short. This would be extremely rare in a covered pickup but happens in an uncovered one. There is a sweet spot with slightly different coil windings where you get some very cool "air" in the tone, especially when the pickup is unpotted and the cover is still on. There is a certain slightly microphonic thing happening. I don't think that is what most chase here...most want that VH1 sound. Go get a Mighty Mite or a Dimarzio Super Distortion and be done with it. Don't believe me? Watch Pete Thorn's famous SL68 vid. But if you want that "Girl Gone Bad" tone, get a good lower dc resistance PAF clone with an A2 magnet and slightly asymmetric coils. For the Panama tone, those here looking at the '59/Custom hybrid and swapping the magnet are probably on the right track...but so much of that tone is the Eventide.
So, Panama, coming full circle, to me sounds like the Frank, with the Eventide being used to fatten it up -- but to be fair Ed didn't remember. It certainly could have been the (then) brand new (as yet unnamed) 5150 Kramer with the A2 '59.