I find this topic very interesting, and here are my thoughts
Bore and stroke regulations would be measured at their MAXIMUM values. so the only way to make an atkinson engine would be to shorten the intake stroke which is pretty much the same as using a much smaller displacement engine (albeit a very efficient one). But still you couldnt make a more powerful engine with less displacement than the best engineers in the world (and if you can, i salute you
)On the cooling side of things providing it doesn't require more cooling there would be no problems, as more cooling ducts and larger radiator intakes means less downforce (thats why the aerodynamisits are always arguing with the engine guys who want more cooling :l) And if it did turn out to run cooler then wahey! its win win
Finally i have no idea if you could get that mechanism to 18,000RPM but maybe, since they are limited these days who knows what stresses and speeds the current engines could manage if they were allowed! Its a very interesting concept and i think you should do more research into it just to see what kind of power and efficacy you could achieve, but the displacement problem is the real stumbling block for its use in F1.
Sean
p.s. you should write to the FIA and suggest that they change the regulations so that the stroke dimensions are only for the intake/compression stroke, to shift the development of engines to be more efficient, making F1 more 'green'
which is the image they so desperately want (as if green stipe's on a few tires are going to save the planet :L)