I've been plaing guitar for about two years now, and this is my set up:

Ibanez GAX70 (has a stock (bridge? It's on the body of the guitar.) humbucker, and a Seymour-Duncan Detonator in the treble slot. I use whatever passes for normal guage strings.

My amp is a Fender Sidekick 40.

I have one effect pedal, it's the signature Dave Donagal stompbox.

I can pull off pinch harmonics fairly well, (Greatest achievement in that department was making my (pardon the distinct lack of knowledge) Low E 2nd fret squeal. Well, squealy foghorn, something.) I only downpick, but I read and printed the lesson on Economy Picking yesterday. Should I learn to alternate pick before this?

The songs I can play so far (in order of learning)

In Keeping Secrets of Silent Earth: 3 (Coheed and Cambria.) -rhythm
46 & 2 (Tool)
The Velorium Camper III: Al The Killer (Coheed and Cambria) -rhythm
Part of Me (Tool)
Black Sabbath (Black Sabbath) -not the main solo, I can play the first kinda solo, however.
Blood and Thunder (Mastodon)- I can play it all, including the bridge. It's choppy granted, but you can tell the individual notes.
Crystal Skull (Mastodon) -rhythm, no solo
Iron Tusk (Mastodon) entirity
Mother Puncher (Mastodon) The second portion of the song is extremely choppy

I listen to progressive metal (Tool, Mastodon, Symphony X, Dream Theatre, etc) and Progressive Rock (This one's mostly Coheed and Cambria.) As you can probably imagine, the technicality of the genre leaves for almost no learning room for a beginning guitarist. Sorta beginning. Mediocre. Anyone have ideas for

A A good second humbucker (something with a sludgy, powerful tone. It's in my bass slot.)

B Good tabs for my (lacking) skill level.

Sorry, but I just had about three months of guitar practice a year ago, and I was only taught bits and pieces of different songs. (Pretty much just seperate riffs.) My theory knowledge is lackluster, as I'm sure you've discovered.
better amp!

Tool out of a Fender Sidekick?

economy picking is only how you go from string to string, something that ideally should be learned at the same time as faster alternate picking technique.

DIVE into online Theory articles. have someone teach you, it helps.

the 'Rhythm' pickup is the Neck pickup, and 'Treble' is the Bridge pickup.
'87 Fender Strat
Oscar Schmidt Archtop
Laney LC15R
Yes, Tool out of a Fender sidekick. It comes out pretty well. I originally used tube distortion and it wasn't bad. What sort of amp should I use? And sure, I'll look through most of the lessons here. Thanks alot, glad I wasn't blasted for my show of stupidity.