Longer stroke = more cubic inches to play with because you gain more on the bottom of the heads. But you also lose a little compression if you make them too long. Gotta balance the needs.
They can be done two ways, a completely different crank (big big $$$$$) or just different length connecting rods. Rods just unbolt and are easier. You might even be able to swap them out by just removing the oil pan on the bottom if you already have the head off. (Hmmmmmm? I wonder....)
I hear that there are also many easily bolt on Cabrillo (sp?)rods available for our bikes too. Jojje (the turbo Swede) has a lot of great information on this stuff. He da man. I know the ones he uses can take over 120hp (so far) without blinking. not too shabby.

A word to the wise is not necessary. It is the stupid ones who need the advice. Pat