So, I vacuum formed for the first time. I have issues like not being able to cut the case out cleanly. I am okay with not being able to use the whole depth since I have two halves to put together. Mainly, I just need clean edges on either side. The problem here is that I dont have a dremel. How would you suggest getting even edge on the middle connecting parts of the cases so I can put them together cleanly? Ive taken pictures of my problems.

I would draw a line around the perimeter with a straightedge at the maximum depth.
Then rough cut with a tin snips not quite to the line.
Finish by using a file and/or a sheet of sandpaper on a flat surface. Be careful, the plastic around the corners is thin and prone to cracking.