I'd like to know where I should go now, in terms of learning theory i.e. what should I focus on next?

So far I have:
-Decent grounding in general music theory
-Recently learnt the notes on the fretboard; not fluently, but I'm getting there
-Don't know much in the way of scales. I'd like to learn them in a way other that simply drilling 'shapes' into my head.

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You're just another brick in the wall
I recommend You the articles written by ZeGuitarist. It Helped me a lot.
Here's the link to his contributions http://profile.ultimate-guitar.com/ZeGuitarist/contributions/
have fun.
And if u don't want to think about shapes hmm Think about intervals, they are the root of theory, i think :P
theory won't do you much good if you don't know the notes on the fretboard fluently. i mean, it'll help, but you'll get more out of it once you're fluent. so that's what you should focus on.

if you don't know much in the way of scales (talking outside of shapes), then what do you claim to be a "decent grounding in general music theory"? based on the answer to that question, you can figure out what you need to focus on next.
If you want to understand scales, start with the Major scale and learn how its constructed, so you understand it in terms of steps (WWHWWWH), intervals (Root, Maj 2nd, Maj 3rd, Perfect 4th etc) and notes (eg G Maj = G A B C D E F#). And apply that to your fretboard. Then learn how to harmonise the scale by stacking thirds - which will teach you what chords come from that scale and the basics of chord construction - then look at the natural minor and how its related to the Major scale, and the pentatonics and how they are related to the Major and minor scales.

You can derive pretty much any scale you'll ever need from the Major scale, so once you get that nailed you've done most of the hard work as far as scales are concerned

Edit: Learn to find intervals on your guitar neck as well - especially unisons, octaves, 3rds and 5ths.
Thanks everyone!

I shall begin right away. B|
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You're just another brick in the wall