Your prints aren’t that far off. I think it should work. I really have no Idea where to go from here. Would you rather just print the new center parts and try again? I had a machine that would sit much further off than yours but I could very easily square it by hand before I started it and it held square just fine. Yours is being a brat for some reason as it isn’t very far off.
Scaling is a bad idea.
Since your parts all seem too big I would try an extrusion calibration, the 100mm one not by eye. You mark 100mm on you filament with a marker or whatever, use the software to manually extrude 100mm in a single shot, then see if it actually went 100mm. The extrusion is the only axis that should ever need calibration. Depending on your extruder setup some are way off (hobbed bolts), the mk style use a gear so they are generally spot on.