Thank you for the information, Simon! Below are some photos for reference, hopefully they help display the situation. It was tough to get a great photo and keep the straight edge straight. I couldn't clamp by the tenon as it has a slight curve to it, but when clamped right at the heel it all seemed to line up.

This is where the gap in the neck pocket is:
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Here are the pictures of the ruler lined up with the bridge:
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The neck has a slight back bow to it, but that should even out under string tension I would think. The ruler lays flat along the frets until where the nut would be where it raises up just slightly. Hopefully that helps show how to get it lined up. Thanks again for all the help!