McCreed, I think you're right - moving the headstock will probably do the trick, but probably downward?
YES!!!
My bad, got it backwards. Headstock downwards to move the low E string in from the fretboard edge.

Based on the other photos, everything seems to line up nicely. I can't say if the sanding you've already done will create an significant gap between the pocket and heel, but there are way of dealing with that if it comes to it. See how you go and it is a problem let us know.

A tiny gap at one side or the other of the pocket is not uncommon, and you can even find that on factory produced guitars if you look closely at enough of them.