Awesome project, I've been wondering what the real world gains would come from atkinson-izing a regular engine in an existing car.
For the valve timing, I seem to remember that there was some discussion about figuring how the valve timing affected the compression ratio in the thread about swapping a Prius engine into a Toyota MR2.
http://ecomodder.com/forum/showthrea...fxe-27266.html Probably worth at least a skim through.