Did you go to preferences, startup-disk and select the newly installed disk as your boot-disk after you replaced the disk? This has a HUGE impact on boot time, otherwise you'll be staring at a white screen after the chime for 10-20secs before the grey apple appears.
There's really no scientific reason why you should have to reinstall your OS to make it boot fast.
I agree that it should make a difference, thanks for the pointer about making it the boot disk. I'm going to clone first then if my results are poor (I could use a fresh install anyway)