Hi Dean,
for 1) - yes. The lower nut allows for adjustment of the height of the pot on the pickguard material.
2) - I would not think a wood screw would work, I would have expected a bolt. Others may know more about this!
3) - I think a small shave would be fine. I have sanded (and filed, scraped) guards around the neck edges to get a good fit. With sanding I normally use paper around a block of wood to keep a straight edge. Take it easy, and keep checking to ensure you do not take off too much.