I'd knock in the 1" bored hole on your South Bend. Then move to the mill. Sweep in the hole so you are one center and zero out your hand wheels. Then move just in the X or Y 1.25" to get to your 2.5"; you'll be moving to 12, 3, 6 and 9 o'clock. I'm assuming you don't have a DRO, so you'll need to take note of the direction you were turning each hand wheel when you dialed in to center on the mill.
If you are making a lot of them, I'd make a fixture for the mill to set the disks in place. Could be a simple 1/4" or 1/2" thick plate of aluminum or steel.
First, locate your mill into the LH side of the fixed jaw for X and the face of the jaw for Y. Then move to the right by 1.5" and down in the Y 1.5" (not critical, needs to be bigger than your 1.25" radius plus the radius of the 4 holes). Set the plate on your mill vise on parallels or a block of wood to space it up (wouldn't want to drill into your vise). Use a 1-2-3 block or suitable edge to flush the LH edge of the plate with the LH vise jaw and tighten it in place. Then spot drill a hole, and drill a tap hole for a 1" shoulder bolt (pic of one below) and tap the hole. You can stack your disks up on the shoulder bolt and tighten it down to your fixture place.
For the four holes, move in just the X or Y by 1.25" (you'll be moving to 12, 3, 6 and 9 o'clock), then spot and drill the holes. Depending on the hole sizes, you could probably skip the spotting step if you have stubby (machine screw) drill bits.
You could also make a custom "shoulder bolt" on your lathe if the 3/4"-10 thread is a challenge. A 1/2"-13 or 3/8"-16 might work fine too. If you go this route, I'd chuck up a round bigger than 1" diameter and turn a shoulder to 1". Also turn the end to either the 1/2" or 3/8" diameter and thread. Naturally, you'll need to do the fixture plate described above with the same thread. I'd cut a couple of flats on the large diameter of the custom shoulder bolt so you can put a wrench on it to tighten the aluminum disks down.
Advantage of the fixture plate is if you ever run the job again, you'll know where the center of the hole in the plate is. Zero your mill on the LH fixed jaw and face of the jaw, set the plate in the vise and flush the edge with the edge of the jaw. Your center will be whatever offset you used to make the plate in step 1.
Bruce