While there is no substitute for a good guitar teacher who knows his stuff, this is a good starting point for theory.
There are endless things to learn: how chords are made, soloing over a given progression, non-diatonic scales, general music theory...the list goes on.
I think that once you ground yourself a bit in any type of theory, you're improvisational skills will grow by leaps and bounds.
Anyway...find that issue of Guitar One!
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"When you're a young, long-haired guitarist, no one takes you seriously." - John Petrucci
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