The pistons should have a "front" mark, either an "F" cast into the pin boss area, and/or a notch in the piston crown. These MUST face toward the front of the engine,or you'll get a piston slap. The piston pin is offset, and if it's installed with the offset the wrong way, the piston "floats" in the cylinder at the top of the stroke, and slams into the cylinder wall when the plug fires. Even if it's necessary to install the rods with the numbers out of sequence, be sure the front of the piston is facing the right way. Has the engine been run with the pistons you're using, or are they new? If they're new, go back to the machine shop and have them correct their mistake.
Jerry