Well, i am not an engine guru. I have played a bit with port timings. I can make a longstroke smooth and a short stroke hit harder than the smooth longstroke. I can do that with crank timings also. I have no explanation of what the stroke does alone and agree that port configuration and timings probebly does more than the stroke/bore ratio alone. Also, rod length plays a part.
Actually, the rod ratio is usually at the very bottom of the list of things that matters. It has gotten a lot of attention due to different car magazines etc as the theory is easy to explain, in very controlled environment like say drag racing you might end up gaining something like 0,001% in some cases, but again it's disproved in the most developed classes.
A lot of these things are debated for full scale 4-stroke engines and might not translate 100% directly to our small 2-stroke engines.
And it's very easy to get caught up in a single parameter so that you miss a dozen of other things that changes as well.
