ShortScale.org

so you think that the binding on the neck needs to be touching the top of the guitar or something?
it doesn't
that gap is wood the white plastic stuff is called binding, sometimes there is a gap or space, sometimes not, but it will all be left up to the bridge position as to wethere or not it will play decently.
*i think thats what you were referring to anyway*

K, thanks for clarifying that. Any thoughts on pickups?

So I've rethought the pickup situation some. I want the guitar to be able to have crunch, but I'm more concerned with the tone and sound and what brings out its strengths the most.

What from the GFS line would you say are best for that?

I wouldn't fixate over the pickups. Get something like this and you can always change them later:
http://store.guitarfetish.com/v59niclalpah.html