Whune, did you order that book yet that I suggested in the other forum? You really should if you haven't already... its right up your alley and you'll love it, I promise. And just to clarify, I'm not saying "get the book, don't watch Christopher's lessons" at all.. I'm saying do both. Its not a "text book" as in "Ahem.. this is how we play guitar.. the first string is E..." zzzzz snore... Its a workbook for the fretboard. It will make clear to you pretty much everything you're asking about... you do these little exercises, on paper, not even with the guitar... and a lot of this stuff will become very clear.
I don't know if you're a Steve Vai fan or not, but if not, you might want to read about him a bit and listen to some of his stuff. Like you, he was very contentious about understanding the theory behind what he played.
