Of course

You can setup a CF disk (for example CF0:) that you can test on WinUAE and once it's ready a simple:
1> Copy CF0: DH0: ALL CLONE
...command will transfer all the CF installation to your real hard drive

You can test it out in an empty partition in case you don't like it much but I kinda doubt it. ClassicWB 3.9 is really awesome
