Re: Your Tone - from the ground up, or from the top down?
Kind of both now that I think about it. It's why I got into pedal and amp building in the first place - I want to know what all the electrons are doing from the time the magnetized strings send them running down the copper coil of a pickup all the way to where they shake the paper cone of the amp.
For me there are two aspects to the final tone - quantitatively you have a certain EQ shape you want in order to sit in a mix well. Qualitatively, you want a particular "voice" - something that's unique to you. To get that qualitative part, it's a combination of gear + technique, emphasis on technique.
I like the way telecasters sound, but they're very bright. I also love how marshalls sound, but they don't always play nice with telecasters. I love the way EP-style boosters sound, but they add a lot of bass and you can't change the EQ very easily. I love how an amp cleans up but to get it to distort you have to run it at ear splitting volumes.
So, my solution is this: I run a telecaster into a jfet-based distortion (with a very low-gain first stage, and high gain clipping stage, with some sag/compression so cleanup is very immediate) which has independent treble and bass controls, into a Marshall 1974x 18w amp (which only has a volume control and a tone control) and a 2x12 with a v30 and a greenback. I also have a wah pedal for wankage and a delay for when I want to pretend I'm Eric Johnson.
My future setup will be the distortion pedal with a more sophisticated clipping arrangement in a wah housing, and a big-box digital delay (in thinking the multiplex) with a rotary stomp switch for mode selection.