Did you ever figure this out??
I'm faced with the same problem.
I have the OS on CD, but no CD Drive.
I have copied the contents of AMIGAOS3.9 onto a CF Card on the PC, and have even managed to make my own boot disk with PCMCIA CF Card support.
So I've installed AMIGAOS3.9
But the problem I now have is that I put BOINGBAGs 1 and 2 on the same CF card and when I try to install those and they both look for AMIGAOS3.9
I can not figure out a way to format the card to rename it as AMIGAOS3.9.
I've tried formatting it using the Amiga, but the problem is, CF cards through PCMCIA only use the FAT95 file system.
I'm stuck here.
How on earth does the PC recognise the Amiga CD as AMIGAOS3.9 if I can't possibly rename the CF card in the same way??