It is all down to how far the holes are from the cylinder pivot and stroke, You can have them lined up at 90deg bit starting to open at 1 degree so there will indeed be a lot of difference in performance so may or may not have the performance to pull your train.

If you can't get the holes the right distance away from the pivot then as you say elongating them is another option I would be looking for an opening of a lot less The ones I have made have opened at more like 5 degrees. Enlarging the diameter of all the holes would also work provided there ports were both closed at TDC & BDC

This is a good example of how the timing will have an effect on engine performance, this engine has a reverser as well as changing direction it also alters the cut off from about 5deg to 45degrees and you can see how much slower and I would imagine weaker the engine is as the amount of air getting to the cylinder is decreased.

Edited By JasonB on 04/03/2021 14:59:11