If these are rebabbited rods, the 1st question I would ask is how were the wrist pin bushings fitted to your new pistons. There are numerous ways to fit the (hopefully) new pin bushings and several of these do nothing to maintain the alignment with the big end of the rod. Sounds like you need to find a machine shop that has the equipment to check your rod alignment. Even new rods need the pin bushings fit to pins. If the piston is tipped enough to visually see a difference or if one piston is level and just lower in the cylinder at TDC than the others you still have an issue that needs to be investigated and corrected. Even if the deck was not machined correctly, it would be impossible to be so far out to have a .015 difference across the cylinder bore, and it would affect all 4 cylinders, not just a single cylinder.