You keep forgetting that a real Mac does not run at all with an 060. FUSION works with the 060 after patching the crap out of the OS and disabling superscaler, and some applications also need the instruction cache off or they will crash. So, the 060 is severely crippled, and thus it should not be surprising that it is a lot slower than 33MHz 040 setup... but hey, what would I know.
People have seen what the Apollo core does on a smaller FPGA with a slower memory interface. You would be rather foolish to be believe that substantially better performance on the Replay is far off.