Since the part has thickness, here is how I would do it.
I would mount the part on my mill table and use my edge finder to find the edges in the x direction. My DRO has a center feature which will zero it a half the difference between the left and right edges. If care is taken to use the same y position for finding each edge and the y zero is reasonably close to the center, a single pass is sufficient. Next, with the spindle set at the x zero position repeat for the y direction. If the x center is suspect, the centering process for the x axis can be repeated. The spindle should now be centered on the part to better than .001". (I can get this to+/-.0001").
If scribed lines are the final objective, a scribe can be mounted in the spindle and dragged across the part to scribe the lines. The accuracy will be as good as your scribe runout allows. To provide minimal runout, dress the scribe after mounting it in the spindle. Perpendicularity of the lines will be as good as your mill. If machining is the final objective, forget about scribing and just go directly to the machining.
While I would use the DRO on my mill, it can be done by the dials with a little more effort. 1st, you will need to account for backlash and 2nd, you need to do some basic arithmetic.