@sbeehre
If you use WinUAE to copy the OS3.9 files, why don't you use WinUAE to install OS3.9, too ?
To get a boot disk, just create an OS3.9 emergency disk and edit its startup-sequence. Remove all the mount commands and insert an assign AmigaOS3.9: hdd:temporary/path instead. (Change it to the real path, of course).
Bye,
Thomas