I don't see the problem at the place where holes start at all. If it is the steppers then you will just see a repeated pattern that is related to the steps per mm and you layer height.

Print a 10 mm square 50 mm high without any holes or sticky out bits or anything, see how that looks.

Print it solid then hollow then with say 15% infill. Do it as three separate prints, not all on the same print.