You should consider incorporating adjustment of one of the X-axis ballnut mounts to gain better alignment of the ballscrew. Currently you're relying on the accuracy of the frame, rail position and all sorts for the distance between the rail and the ballscrew to remain constant. In reality the tolerances on all these build up, so it's easiest to make sure at least one of the bearing mounts (clearly the non-driven end is easiest) position is adjustable in the Y-Z plane to ensure you can align it accurately. If not you risk the mechanism binding towards each end which will put a large force on the ballscrew/nut...

On my Z-axis I currently have 520mm long 20mm NSK rails, so the additional height of those helped. If you go up to 25mm plate for one of the plates on the Z-axis that might help to get the required pocket depth without sacrificing strength. Using that strategy I recently made a Z-axis using 25mm profile rails with only 2mm clearance between the plates. Also if you get the Z-axis parts machined there's not really any need to use the more expensive tooling plate - I would mill the surfaces for the rails and blocks to get them flat and in the same plane.