Hi Phillip,
Your thinking is correct. The piston should not go past the cylinder ports but without knowing the position of the ports or pistons, it is difficult to comment. (a drawing would help). To get the maximum efficiency out of the engine you should utilise as much of the cylinder travel as possible with a minimum of clearance at each end. (Some clearance is needed to allow for expansion and steam flow).
If your piston rod is only a couple of mm too long and the piston is not bottoming on the end cover, it would suggest that the ports are in the wrong position or needs a notch cut out as Jason suggested. As long as the piston still seals before the notch.
Paul.
Edited By Paul Lousick on 08/04/2018 10:52:49