Since I am staining, I used elmers stainable wood glue on the mitred edges, then I used a bunch of L brackets with wood screws to make it square. Worked great! My plywood had a little bit of a bow to it and the L brackets and wood screws helped pull everything back to square. Afterwards I used stainable wood putty fo fill my edges. Now I am ready for a stain! Hopefully it takes the stain well, I am worried about the putty taking on more/less stain than the plywood, but I figure using a wood conditioner should make it all even.
Thanks everyone!