Dave,
in this case I just leveled the case using a dial indicator mounted on the quill, and centered on the bearing bore. Since the sleeve is concentric, all I have to do is repeat the process for the final boring.
When I first set up these cases back in the '80s, I had to bore the main bearing boss after welding, because welding the reinforcing plate around the seal area had shrunk the bearing bore when the weld cooled. At that time, I set up the timing side and indicated off the dowel pins to find the coordinates of the bore in the timing side, then did the same with the drive side and bored it to match. Since I already know the bearing bores are in line, all I have to do for this operation is indicate on the existing bore to find the center.
It would be nice to be able to line bore with the cases together, but that would involve making more tooling, and my current method should keep the bearing bores in line within .001" or so, which well within the mis-alignment specs for these bearings.
Ken