12:05 Garage- ’70 Duster build

Yes, the longer shoulder on the studs is what centers the rotor on the hub. I don't recall the part number studs I used, but those look like them. The lug holes in the rotors are quite large. I want to say they are around 5/8". This is another reason I wanted the shoulder because the rotor would have been able to move on the threaded portion of the 1/2" stud. The .0275" difference in the bolt pattern is easily overcome by large holes in the rotor. What I should have done is had the center of the hub turned down to match the center hole of the rotor. I don't recall the size difference but it wasn't much. I just opened it up with a die grinder and sent it. I didn't put a dial indicator on the outside of the rotor, but I did spin in it while closely watching the clearance to the caliper. My eyeball measurement showed zero runout and I have no vibration.
I think you may be overthinking it (not a bad thing). If I were to do it again, I'd turn the OD of the hub down a touch so the rotor fit perfectly. Other than that, it's quite easy. If I remember correctly, the Mustang rotor center hole was a bit smaller also.
I did consider drilling and tapping the rotor/hub to hold the rotor on, but it didn't seem necessary after everything was fit up. The brake pads pretty much hold the rotor in place when the wheel is off.

The rear rotor must have a different size pilot bore.

The front rotor has a center bore that is bigger than the unmodified snout by about .03" overall. If the hole were smaller, I would get the hub turned to match whatever the size was on a Challenger, but being that it is bigger that doesn't work. And being such a small amount I can't just grab a ring that is 2.85" OD with a wall thickness of .015" as I doubt anyone can make such a thing. Which is why I looked at centering it using the chamfer on the inside of the rotor bore. The more I think about that, the less I like it since it probably isn't held to a very tight tolerance by the rotor manufacturers so even if I get one to work, a replacement might not.

The hubs I am currently running have been turned down to 2.80" at the hub flange to match the '98 Cobra rotors. But even then the difference is only .05" overall. The snout of the hub was turned to 2.78" OD to match the Mustang wheels I am running, and if I got the rotor pilot area turned to that OD as well, I would be up to .07" difference overall.

Maybe I should just grab a .015" feeler gauge and stick it in the gap and leave it there. Or use the hubs I am running right now and a .025" feeler gauge.

The most annoying thing right now is that if I had chosen the GT500 calipers and rotors instead of the Scat Pack ones, I wouldn't be worried about it as the center bore on those rotors match the Cobra rotors I am already running. And in the end it looks like the GT500 caliper would have been easier to build a bracket for as well. The narrow mounting hole spacing on the SP caliper makes it really tight with the spindle holes and only works (best I can tell) with a 14.2" rotor or bigger. Ah well, 20/20 hindsight.