1) The biggest concern I would have is the bottom end of a 500 up to the additional horsepower and torque
2) It might be more economical to find a used complete engine and sell the one you have to offset cost. That is if cost is important, which if you are involved in this sport, I would assume itís not.
3) I understand the math involved in getting to the shim height, but I would think you would need to take into account gaskets on either side of the shim so that would make the shim quite thin assuming 2) .5 mm that would leave you with a .8 mm shim. I guess you could plan on shaving the head, which would allow you to use a slightly larger shim.
4) Your right about the 40mm carbs. They are readily available on E-Bay. You could even try them on the 500 you have now.
5) Changing the rotary valve although not necessary may be something you might want to consider. I bought a carbon tech fiber rotary valve for my 670. It has a very similar opening to 501valve that many on this board talk about all the time.
I have probably raised more questions than I have answers. I might not of helped but,
There are a lot of people on this board with a lot more experience than I. I am sure someone will put their 2c in.
Good luck with the project if you decide to do it.
Just to make things more clear than my earlier post, I don't only want to install the cylinders. It will be a complete top end including head, and exhaust (with center spiral dump)
I need more advice like above. Come on guys, be the devils advocate. Try to shoot down the project, try to come up with as many reasons as you think its not possible and we will try to find answers to each comment.