My advice would be to ensure that all the Main Bearing parent bores are cut in one operation, (This has been the practice in Industry for MANY years ) with one tool. In this way, they will be in line, and the same size.
Setting multiple tools to the same size will be difficult, so why introduce extra complication and risk, needlessly?
As Jason says, make the boring bar as large a diameter, and as short, as is practical. This will maximise stiffness, (less tendency to whip/deflect ) and accuracy, as well as reducing the risk of chatter. Rough out with a drill, and finish to size with a stiff Boring Bar. (If need be, set it up on consumable material, ready for use after the roughing operation )
Howard