How to initialize an IDE drive mounted as a "SCSI" drive in Basilisk II. (Note this was done with Windows 98SE!)
1. The drive must appear by name (from the drive's firmware) instead of Generic IDE in Device Manager, which means Microsoft's IDE drivers won't work. You must have buss master drivers for the IDE controller. VIA took a long time to get theirs stable. Intel's are hard to find on their site for older chipsets and old versions of Windows. Newer Intel chipset drivers for them simply say the chipset is already supported by Windows instead of installing the last Intel driver release. (NT based versions of Windows always show drives by name so this shouldn't be an issue.)
2. The drive needs to be FDISKed as a single FAT16 partition but NOT formatted. Windows will take control of formatted hard drives. I don't recall what happened when I tried to access a completely unprepared drive with Bailisk II, I just remember it had to be partitioned but not formatted.
(I've no idea if Windows 2000/XP/Vista/7 will block Basilisk II or Sheep Shaver from accessing a partitioned but not formatted drive.)
3. In the GUI, enable SCSI and select the "SCSI" drive you're going to use.
4. Use a patched version of Apple's HD SC or Drive Setup to format the drive. No other utility will work because Apple's is the only one which works entirely with System calls. 3rd party formatters use some direct hardware access which Basilisk II and Sheep Shaver do not emulate.
5. Make the whole drive one partition. Attempting to do two or more will crash it. I never tried making more than one partition with FDISK for this process. I don't know what Apple's drive utilities would make of the DOS/Win extended partition setup.
The base structure of FAT16 and FAT32 must be identical or very close to HFS and HFS+. I found that the easiest method to use a SCSI drive not supported by Apple's utilities on a real Mac is to FDISK and format on a Pc using a good SCSI controller. Hook the drive up to a Mac that has support installed for DOS disks then simply use the Erase command on the menu bar to change FAT16 to HFS and (in OS 8.1 through 9.2.2) change FAT32 to HFS+.
Soooooo... who wants to try making an IDE or even SATA drive work with Sheep Shaver in Windows XP or later?
I assume that with Basilisk II a 2 gig maximum FAT16 unformatted primary partition would need to be created at the start of the disk. Dunno if the rest of the drive could be formatted and used by Windows afterward without fouling up the Mac partition.