So you "replaced the axles".
With what? New axle shafts? Do you still have the old ones?
You're going to have to take the wheels off and indicate the axle flange without a brake rotor attached. Rent or borrow a dial indicator with a magnetic base to get this done.
You can also use the indicator to check axles for face run-out on a bench with some V blocks.
I suspect the chances of having two sets of axles, if we understand you right, bent to that degree are slim.
Check how the brake rotor sets on the hub flange, then how the wheel interfaces with the rotor.
You may well find an issue there.
Or it could be as simple as torquing down one lug fully with all the others loose causing the wheel to set crooked.