The machine my unit had was equipped with a 4 axes servo system. We had the 4th axis motor on the mill lift and in some cases we used it for what you are describing. To maintain the best accurracy, its always good to keep as much of the quill inside the casting as possible. So we would lower the mill as close to the part as possible to minimize quill extension. If we needed room to change a tool we would raise the mill up. We built a brace on the 5th column so there would be no lateral flex when the mill head went up and down. We also added a magnetic type scale to the mill head so we could return to the original position after changing the tool. We also had the servo driven rotary table, and when we wanted to use it we would just unplug the mill lift motor and plug it into the rotary table. You could do the same with your machine- I would suggest, first get the quill centered to the lathe axis, then adjust and plumb the 5th column and add a brace to keep it positioned. I think you can find those magnetic scales at www.enco.com for about 50.00 - get one with about 10" travel.