Actually, rod length usually has very little to do with the equation (If you don't change it), only in a V-type engine configuration where internal balancing becomes more dificult and counter weight interferince is a problem at times. On a four cylinder engine like the sohc4s, balancing is very simple because two pistons go up when two go down, canceling each other out. The same is true with most of the honda twin cylinders, one up, one down. The rod length comes into effect when you take a crank and offset grind it to become a stroker crank. A very expensive and timely thing to do. In fact I have not even heard of this for motorcycle applications since there are many, many more problems with interference issues and machine work and even more time and money that the end performance gained do not justify the cost. The other option would be to buy a stroker crank. I think it is safe to say that if you can buy a stroker crank, then you can get pistons and rods to match the application so the only problem would be to clearance for the extra stroke..............
Anyway, I could go on and on talking about those sort of things but I may bore you in the end. I just love machining and building engines and I would also love to pass along my vast knowledge on the subject and many of the things I learned while getting my machining certificate.
Back to the Hondas: Most of the piston designs are similar enough to mix and match to get a custom engine combination. The piston skirt is designed to clear the counter weights in its original application and that is definitely something you have to look at when mixing parts. Machining the pistons a little more to clear a certain crankshaft is not hard to do by a good machinist but it can be hard for certain person to look at a piston and see if it can be done. With the CB500 pistons in a 250 Rebel, the piston requires no machining at all. The distance between the piston pin and the skirt is just about the same on both pistons, enough that no machining is required.
The compression height, as it is called in the machining world, is what I believe cb650 is talking about with the "Crown Height". That is the distance between the piston pin and the piston crown. This is probably the most important part of custom building because it can not be fixed or changed as much as the skirt problem can be. Several thousands can be removed but none can be added and if it is too low than massive head shaving must be done, or a very low compression ratio will be the result. The only other way to fix this problem is to add a longer conecting rod to the mix. The rod must be the precise length and piston pin diameter must be the same as well as the journal size. It is very tricky to find a rod to work that came from another bike because these measurements and specifications are just not out there and are very hard to find if they are. As you can see it is a very timely process to figure out a custom combination and many hours of research are required just to get started. If any of you have maching questions, feel free to ask me. I will always be happy to share some knowledge.