Who told you you could use your CNC router as a lathe? Are you talking about putting a piece of wood in the spindle and fixing a tool to the bed? That won't work for a number of reasons.
Or did you mean that you're adding a rotary table for a 4th axis? That won't make it a lathe, although you can make radially symmetrical parts that way. In that case, the simplest thing to do is to put a clamp on the Y axis so that it won't move, position it at the center of the A axis, lock it down, and transfer its cable to the motor on the rotary table. The new configuration would be XZA.
Andrew Werby
www.computersculpture.com