Easiest, and first step if I were to check it would be to indicate the existing holes on the mill to see if they're parallel to the receiver centerline.
Checking to see if the receiver threads are concentric to the bolt raceway, and whether the receiver face is perpendicular is more involved.
Receiver face needs to be chucked up with a mandrel or receiver holder fixture to be indicated and skim cut if needed. Then, I clean up the threads with a receiver tap, and run a precision threaded mandrel into the receiver. When the shoulder of the mandrel is threaded up to the receiver face (lightly blued) it should show full, even contact. If not, gap checked with feeler gauges and if over a couple thousandths exists, the threads need to be recut.
Opinions differ from there. I have recut threads without cutting them oversize with excellent results. The threads can be a tiny bit "sloppy"- but what really matters are the mating surfaces of the receiver and barrel but being perfectly true and concentric- that's what positions/locates the barrel, not the threads.
Others will tell you that the receiver threads will need to be cut oversize, with a new custom (oversize thread) barrel to match.
Hopefully, it's just your mounting holes being tapped off-center. Easier " fix", but still not a simple fix. Holes that are "off", need to be plugged, the re-drilled/tapped in correct locations (and may as well go to #8 while you're at it).
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