I think I would join the top and bottom halves with the two 5BA fixings while laid on their sides on a flat surface so they stay lined up. Then mount the them in the mill vice with the bottom bearing against the fixed jaw (previously clocked true) and a packing piece between the two 5BA fixings so the moving jaw can bear on the cap, you will probably need to raise teh work off the vice base with parallels.
Drill and bore the first then use a stop set against one end so that when you put teh second assemble into the vice you can locate it in the same position.
This sort of thing
