Adam.....I just told you how to fix this, so did idch. Do you not understand what I said?
Take a router and a template and make the neck pocket even, flat, & perfectly square etc. THEN take another piece of mahogany and shape it so it is an exact fit for the neck pocket, leave it a bit snug. Glue it in, clamp it and let the glue dry. Now take a template for a neck pocket, using your router, route out the new neck pocket.
Is there something that you do not understand about this procedure?