Is your 4" CRS stationary? It looks like your extrusion is bolted to the carriages that move on the Gantry, and that your 4" CRS is is bolted to that in a stationary position... then your Z carriage made of two standard bearing carriages and a high Z plate move up and down on that..
Have I got it right?
If so, you've lost all your Z travel.. You won't be able to get hardly any clearance under that fixed CRS rail...
You need to not only allow for various thickness materials, but vacuum system, and hold down fixtures..
If you really plan on building a machine with only 1" or so of available travel in the Z direction, then I would shorten everything up and move that gantry right down on top of the X rail carriages.. thus reducing the twisting forces on the gantry... If you're not gonna use the extra travel of your Z fixture, why introduce extra force?