Hi,
I also did this (via hard drive!) before I got my A3000's CD working properly.
I LHArced the contents of the OS3.9 CD (less the videos and other fluff) from within a WinUAE environment, then copied the resulting file directly to the A3000's hard drive.
This preserves all the protection bits, plus upper/lower case filenames, and also avoids the problems Windows has with copying files called "AUX" (it's an MS-DOS legacy device filename).
Once you've got the LHA file on the Amiga, you'll need to unarchive it, then create an emergency boot disk - which you'll then need to modify so that the right files / assigns can be found.
- Ali
