ok, gonna try to explain this without being too long winded (and perhaps someone more knowledgeable will be able to add more)
When you change the stroke, you change when the piston covers/uncovers the ports. without changing this you'll have a motor that runs poorly. the ports need to be covered/uncovered at certain points.
the really important part is getting the exhaust port right, and getting the exhaust port matched to the pipe you're going to use. I really love my f7/powerpros/ct/trinity pipe. lots of power all over.
i also think you will want a bigger carb with that setup, something around the 33-35mm range, especially if you're duning.
another thing is that the head will need cut for the crank, and you'll need to have the cases trenched to clear the rod. something that's a little more drop in for you would be a vito's +3 crank, won't need trenching.
another thing is your builder should really have all of the parts that you're going to use to port that top end, that way they can accurately match the ports. it'll be interesting to see what they do with that cool head setup.