Dangerous Territory

After a long pause, and due to the nature of the work i have been doing over the last few years, I want to delve into the debate about whether or not tone woods and guitar construction in general affect an electric guitar's AMPLIFIED tone. I know this subject is fraught with peril, so I want to be really careful.

Without question though, one place where people get jacked repeatedly comes from the attempt at chasing the dragon of that elusive magic guitar tone! We could all probably name several examples of outright fraud being sold to the aspiring guitar player without breaking a sweat. I am far more interested in what the science and logic in general have to say. I realize that a great many, perhaps the majority of people selling these claims actually believe them, so they aren't necessarily being malicious, even if they turn out to be untrue. I know this subject can ruffle some feathers, and I'm not really known for staying away from controversy, so this could get ugly really fast. Please try to keep in mind that offense is taken, not given.

I want to make it clear, hopefully as I did in the allcaps above that i am talking about the *amplified* tone of an electric guitar.

I'll say it again: I am only interested in this discussion in the signal that appears on the guitar's output jack.

So what are the claims I'm looking at?

1. The type of wood used on a guitar affects the electrical signal the guitar generates.
    a) The effect the wood has on tone directly
    b) The effect the wood has on mechanical qualities like sustain, which of course could also lead to a tone change

2. Bridge and nut materials (or locking vs standard nuts) affecting the tone. Here we can get into some insanely expensive stuff like the titanium replacement blocks for Floyd Roses (sheesh! Only 460 dollars for this guy! http://www.fu-tone.com/catalog/index.php?main_page=product_info&cPath=66&products_id=198 )

3. Construction methods (bolt on, set neck, neck-thru, etc) and their effect on tone

I really want to know first if there's even a mechanism for audibility, and one I keep stumbling over is the phenomenon of microphonic pickups. There may be a "there" there. Whether it passes the threshold of audibility in common use is another matter.