I shudder every time I see someone suggesting using the calibration routine in Mach3! If the machine is giving errors this big, then you need to find out why, rather than hide it under the carpet. You are using ballscrews which are almost as accurate as your digital caliper. You know how you have geared (if not 1-1) your motor to the ballscrew. You know what microstep setting you have used. This gives an exact "steps per" value, and if the machine isn't achieving this, you really need to find out why. For example, it might be as simple as needing to check the adjustment of the ballscrew support bearings - and whether they were assembled correctly in the first place (don't trust the Chinese to get this right!).

Double-check everything first, including actual cutter diameter (I spent ages chasing machine errors that were down to cutter diameter errors, although that's not the case with differing errors in X and Y), and don't panic. You'll get to the bottom of it with a bit of systematic testing!

Good luck - we've all been there.