Some hints:
- the better way to use virtual harddrives is to enable RDB mode and use HDToolbox to partition them.
- you should use VHD (tick "dynamic HDF") instead of HDF. With this you can make much bigger harddrives and still save a lot of space on your Windows harddrive.
- as OS3.9 is your goal you don't need to make the detour through OS 3.1. You can boot WinUAE from the Emergency-Boot directory on the OS 3.9 CD. Then create an emergency disk and continue as usual. Some manual changes need to be made to the emergency disk, though: kill the write protection bits and correct the emergency_cd driver.
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Edit: forgot one important point:
- when formatting a harddrive, no matter if real or virtual, always use quick format. Standard format only produces hot air and wastes a lot of time.