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Should I worry about this?

I'm putting together a Warmoth with a geddy neck and the holes in the neck are between 1/4 to 1/2 of the hole's diameter off from the holes in the body when its in the pocket.

Should I try removing some wood from the back of the pocket in order to slide the neck in a little more or should I just fill the holes and re drill?
 
Your best bet would be to find some nice dowel and drill straight, clean holes that the dowel will just fit into. Then glue the holes, press in the dowel, and wait. Cut off the excess (leave a few inches proud of the surface to act as handles while you press them in), sand, and re-drill.
 
Well, I'll caveat what grisezd wrote by saying that were this a guitar I was working on, I'd cut a dowel from some maple (or whatever wood I'm working with) and use those. Commerically available doweling is usually longitudinally grained, so when one inserts the dowel as a plug and then drills into it, one will be drilling into end grain - not the strongest choice for a screw bed. Ideally, you want to drill into side grain, and making your own dowels/plugs from stock with a plug cutter is best. However, that said, I've used the end grain type dowel method on cheap guitars I don't care about and they've never failed, so really it's your call...