Well I ended up pulling out the Dremel and started hacking away since it seems there are no other options in dash kits. All I had to do was cut out a few notches on the corners to make the kit flush.
When I first put the deck back in the dash the bottom was flush but the top was still recessed a bit. I remedied this by adding a few washers on the top two screws in between the mount and the dash to make it stick out further. Figured I'd share with some pics for anyone else that might run into this issue.
Now it looks nice and clean!