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I have tired to print a specific file 3 times now and it keeps coming out mirrored.
is there something in the CL-60 firmware I need to fix
You probably have your X direction reversed. Try changing this value in Marlin: INVERT_X_DIR. If it's set to false make it true and vice versa.
its actually the Y axis, because you home to the Y max, I think
Yes, only you would know that because I don't know along what axis your prints are mirrored. I was thinking in the lines of "mirrored" = flipped along the X axis, "upside down"=flipped along the y axis. And homing has nothing to do with a mirrored print.