Retrofit Backlash

I'm converting new Taiwan 9x49 knee mill to CNC using Ball screws and
steppers.
There seems to be .001-.002 backlash in the X, .001-.003 in the Y and
.002 in the z. It seems the backlash is coming from flexing . I put a
indicator on the yoke up inside the casting to check the Y and it
seems to .0005 backlash to there but when I indicate at the table it's
a different story. I have the same problem with the Z. I couldn't get
a indicator on the yoke to check the X.

Anybody have this problem or have any suggestions.

TIA
Geo.