I only skimmed this thread, my ADD got in the way.
Lots of factors affect tone. The biggest one? HOW I FEEL THAT PARTICULAR DAY! Some days I'm "on" and it's right there, other days, I'm not, and it's not.
Tone is primarily in the fingers (amps help too..) That's ALL the vast majority of folks ever notice. Jimi would be Jimi playing an Indonesian plywood strat, just as Duane would be Duane playing a Hondo. There's a noticeable difference most of the time between single coil and humbucker guitars, BUT the inconvenient truth is that the guitar is the LEAST of it, well behind the player, the amp, and the processing. We care about our axes because we're players, but as the owner of 80+ guitars, I can tell you the main difference is how I'm feeling, and my amp choice.
IMHO, scale length (which determines string tension at pitch) makes as much of a difference as pickups. But your larger point - tone is largely in the hands of the player - stands.
I own many guitars as well. I suppose I buy guitars, pickups, etc. in the hope that this one change, this one last piece of the puzzle, will somehow transform me into some kind of guitargod. Never seems to work - all this gear, and I m still me.
Throughout this discussion, there seems to be an assumption that "tone myths" are in fact "myths". Until proven or disproven, through double-blind testing or otherwise, "tone myths" should properly be labeled as "tone theories".