Little update on the Z and Y cartdesign, after a lot of iterations i'm now converging on a better solution for the design. However there are still changes to make and improve upon, and I hope on some feedback on my design.

A image of the whole thing. With the 100x200mm t=6 steel square tube in the front.

New setup on the stepper motor for the Z axis with a belt and pulley system. The Stepper is also mounted so it's easy to tighten the belt. It's also easy to pluck out of the machine.
The end of the ball screw it fixed with a custom double ball bearing fixture. Using 10mm thick SKF 6201 ball bearings.

Njhussey, after some back and fourth I managed to make space for the Mounting of the Z and Y blocks over each other.

Here is the square tube see-trough so it's possible to see the mounting of the spindle and the ball screw mechanism. I had to make a cut in the square tube from the top to make space for the ball screw. This did not however weaken the rigidity of the Z cartsignificantly.