here's another one i've read several times...taking the cover off a humbucker makes them 'brighter' or more 'trebly'.
i think there is something to the 'neck thickness' idea...how much, i don't know. i read something on Bill Kirchen awhile back, and he claimed that necks had a lot to do with sustain.
i have no clue...i have found out that each guitar i have likes a certain amp setting. another guitar may not like that amp at all-or i have not found the setting yet. the epiphone valve jr. i have is an 'individual'. there is a setting somewhere for everything i have, but it may be counter intuitive, and i t may be 'one setting, one tone'. amps are a trip unto themselves.
Kirchen also said he loves the new jensen neodymium speakers...that got me hooked, too. his tone on 'Smoke, Smoke, Smoke that Cigarette' is outstanding, i think. another speaker myth, connected to pups is 'alnico sounds sweeter than ceramic'.
another 'myth' i have read is cables make a large difference. i can't prove that one. lots of people have better ears than i do.