Once you have your boxes straight a la Finsky method, use a square ( commonly called a rafter square ) and, well, square your boxes.
After they are perfectly square make youself a " jig " using a suitable piece of plywood larger than the supers, with the super placed on the ply, glue and/or nail/wood screw some strips of wood around the outside perimeter, snugly, of said super.
There you have a perfectly square " jig/form " for future box construction.
You can also screw some strips inside the box and voila you have a jig/form that will keep the walls of your supers upright, straight and square.
Now once all the woodworking is done, take the form/jig, declare IT a piece of art, hang it on the living room wall and now it's doing double duty.
This is one occasion where YOU want to " A SQUARE "