Like many Prusa-like designs, you have no structural component on the X-axis, so the linear guides have to do double duty. How far do the smooth rods recess into the Z carriages? If they don't extend most of the way across the carriages it is likely that you have significant amounts of flex in the X axis, mostly in the Y direction, as well as the usual twisting of the axis that plagues this layout. What diameter are the smooth rods? The standard 8mm smooth rod has a remarkable amount of flex to it. If you hold a Z carriage in each hand, can you flex the X axis back and forwards by twisting the carriages? If so, it's time to redesign your X axis for more rigidity. Flex couples are next to impossible to get well aligned, so unless the Z and X axes are extremely robust the off-centre rotation will force the head out of position.