I printed another cube slower this time, with the same rest of the settings. I also marked the shafts. After the print, the shaft and pulleys were still aligned. There still is an indent on the bottom side of the x-face and the opposite face, although the indents and wavy patterns are different on the cubes. The cube on the left is the one printed at the normal speed recommended on Cura, and the cube on the right is printed at a slower speed. I don't know if this is a significant improvement, is there anything else I could adjust other than the speed?