Hi Tvalenzuela1432,
To be sure, you can do a cutting test just by doing a punch of 10x10 and 20mm thickness, measure between faces with a palmer and if the difference is below 0.008mm should be OK. That means that geometrically machine is fine, but if you repeat the test on another place of the table the results can be different and the ballscrew could be more damaged in one side more that another. Just take the place in the table that goes better.
If you want to solve your problem you must decrease the offset in 0.0015, because the offset is radial. With this the wire would go near from the workpiece and do it bigger, just do ALL the entire program rough and skim because it seems to be few microns but could be contact.
Regards.