You should increase the spacing of the Y-axis rails to reduce the force on each and thus minimise deflection of the tool parallel to X. It would be good to increase the bearing block spacing on Y for the same reason.

It may be difficult to align the Y-axis rails since the spacing is defined by the width of the machine frame, so if that is not cut extremely accurately it will not be parallel. You've not got any way to adjust the spacing. That's why most people mount them the same way up, not facing, on X, although if you can keep the same orientation the average stiffness will be greater.

Also I think you can get the X ballscrews slightly closer to the X-rails. That's not going to make a huge difference, but if you can there's no reason not to.

Hard to tell from the images, but is how far the spindle sticks out limiting the travel on X?