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I think the biggest problem is the SHCS. Its just too big. I think if we used hex bolts instead it would be better. Also if I were forced to use SHCS maybe it should be counter sinked? Not sure if theres enough material. I think changing to hex screws would be best. As for material I had to remove, maybe about 1-2mm on the specific areas where it rubs. But I think its rubbing only because the cap screw heads are long. It all boils down to tolerance by the bolt manufacturers. I wouldn't change your design just yet until someone tries the hex bolts. For the pistons tho, theres no point in leaving the tolerance so tight. I would reduce the diameter by 0.5mm . If someone scaled it down, it would introduce other problems.