Some thoughts:
- You could use a thick gasket to solve the problem but would lose the centring action of the step on the top plate ... probably not too important. Whether a non-metallic gasket is viable depends on whether the engine is single or double acting and the pressures.
- I presume the piston tightens onto a shoulder so you could file that back 3mm
- Could you reduce the stroke by moving the fulcrum or changing the beam length?
- You could enlarge part of the hole with a jobber drill and accept that the nut tightens onto a sloping surface, or you could make a suitable washer
- Could you bore a recess in the cylinder end?
Finally, if all you have is a hacksaw, and no mates with a pillar drill, drill stand or lathe, then I suppose you could saw a few mm off the piston as a last resort.