Any kind of mark on the cylinder walls other than the correct cross hatch hone pattern will have an adverse effect on ring seating and break in problems. Did you mean to say you can't move the rod back and forth on the piston??? If that is the case, you need to have the rod, pin, and piston checked at a competent machine shop. At the very least, the block should be rehoned to remove the "stains" on the walls, new engines hate any type of contamination.!!!!!!