Im understand that the grooves in the side bricks are cut all the way thru to the back leaving holes in the back wall but I'm not following you on how you propose to fix it. If you could remove some top bricks and let me see what you have going on in the back I'm sure we can figure something out.
As for the door, rabbit a 1/4" groove all the way around the inside of the door bricks where they touch the door angle iron. That will inset the door bricks so they mate up to and touch the wall bricks.
Like this
