Are you sure this is a worthwhile endeavour? It seems WinUAE already provides a good level of hardware compatibility.
That aside, one technicality caught my (sleepy) eye.
I would assume cycle exact emulation would preclude technologies such as JIT since Chipset v CPU dependent timing issues are lost in the translation.
I dunno if this is really a problem or not but it could affect time critical writes to your virtual chip ram/custom chip regs...
