To check the alignment just use a caliper and measure the free end of the ballscrew to the casting in both dimensions with the saddle at both ends of its travel. A small difference is fine... but if you could measure the difference with a tape measure there is a problem If there is an alignment problem you could drill out the holes on the mounting plate (or drill new holes) and/or put a spacer under the ball nut mount.

If it is binding at both ends then perhaps you have a combination of a misaligned ballscrew and tight spots on the ways...