Depending on how much the difference is it could change the CC of each cylinder if the valves are SUNK different on each one. Lets say Cyl #1 is 62cc and Cyl #2 is 65 because of the difference you would have a different compression in each cylinder. Not that you couldn't adjust the Rocker to compensate for different valve heights. Even so still the CC of each chamber would be different. Since it is not a super crazy build I don't know if it would matter, better to ask a machinist/engine builder like Brian at IMM. He also has other issues of the Rocker arm hitting the Retainers on some of them. I would say the spring heights are different proving the theory that some of the valves are SUNK into the valve seats more than others.