I would suspect that the cracked z-axis support is going to cause and issue and should be replaced. Even if it doesn't, any small issue you have while testing the printer will result in 'umm, I wonder if it is caused by the z-axis support' type of thinking. I would replace it now.

On the benchy, is it a repeatable shift ( i.e happens at the same point )? If so, I would think on close observation of the movement of the print head thru this height you could see the shift. Try a simple rectangle print and see if the issue appears.

I would not think that it is the SD card. You could always copy the gcode back off the card and compare with the original.

Octoprint - just installed it on my RPi and connected to my K200. Love it.