pyramid/piston port have way different internals than a flat reed. the output sprocket and pedal mode engagement system is radicaly different for starters.
I wouldnt worry about the 6500rpm figure, that goes up drasticly when you stop using the stock cylinder.
swapping cranks could change the stroke concievably, I've never compared the two styles side by side.
hey jude, im using that gilardoni i got off you on my laguna btw.