So I've been playing for 14 months, and have been really itching to get into what makes music sound like music- chord progressions, scales, modes, and all that fun stuff.

But where do I start? I bought this book called "The Guitar Grimoire", the scales and modes one... and while it seems chock full of interesting scales, how do I apply them to regular lead playing? I already know what intervals, half/whole steps, and transcribing (a bit; my teacher had me transcribe the chords to a Eric Clapton song into a different key) are, so I guess I kind of have a start, but I think I need a push in the right direction, especially since the music I want to play and write (melodic metal, neoclassical, and progressive metal) all need a good dose of theory (or so it seems).
Guitar Grimoire is not the way I'd recommend that you learn, if I remember it just lists a bunch of scales but doesn't explain the theory well enough. I'd pick up a copy of The Complete Idiot's Guide to Music Theory; it's a great book.
I started learning stuff in this order:
Triad construction
Chord progressions
Improvisation (non-modal)

After you learn to improvise a bit, everything will come much easier.

Also check out videos like Melodic Control by Marty Friedman, he explains improvisation and scales and arpeggios.

It might not work for you, but it did for me.
i swear there must be at least one other thread on this right now.

even if you don't use the searchbar which would give you tons of answers just look at the first couple of pages.
I'm learning the same thing right now...

The way I'm doing it is sitting here and I just think a note... I'll think of G for example. Then I'll play all the Gs I can remember, and go find the ones I cant..

third fret - both E strings
fifth fret - D string
12th fret G string


Also, I'll play something small, like a tiny lead. Maybe 5 or 6 notes. Then I try to think of what notes they are. Then move the lead to a different octave.
"Guitar Logic" is a great book it assumes that you know nothing goes over very basic things like how read time signatures and what the differnt value of notes are etc.. it teaches you key signatures and chord progressions and the whole back of the book is chord scales and scales in different keys and it has an interesting way at looking at modes as well called the conveyer belt which i havent heard anyone on here talk about yet. I didnt finish the chapters on that stuff yet so i cant explain but its definatly worth picking up for 20$ if your just starting with theory.
for learning notes i had a 7 day schedual i did. i would on day one go up and down all 21 or 22 frets of the low E counting #'s and b's such as G#'s in one direction and Ab's in the other, then switch it just to be back and forth familiar no matter how im playing. just the low E, nothing else. keep it simple. day 2, A string and so on, then day 7 all 6 strings. do that for 2 or 3 weeks and you'll know every spot on the neck w/o thinking.