Im no expert, but your Y axis will be working against Gravity in one dirrection and not the other so (Im assuming the spindle will move relative to the table) the traveling portion needs to be as light as possible. I consider having the Y axis guides mounted away from the table (some sort of frame) and only a crossmember (X axis Guide ) that moves in Y.
What kind of arrangement did you have planned ?
Backlash in Y shouldnt be a problem .