Your problem is actually very easy to fix:
If your system has 2.0+ ROMs, you can boot boot off the 2.1 disks and use HDTools with no problem. The reason HDToolbox is not working is that the scsi TOOL TYPE is incorrectly set. SCSI_DEVICE_NAME=scsi.device should be changed to reflect the correct scsi controller. If your system has a GVP SCSI controller, it would be gvpscsi.device or omniscsi.device (if you have a GURU rom installed). The original disks simply have scsi.device entered. If you are not using this controller, it will not find it. Make sure that the case is entered correctly.. for example, gvpscsi.device, not GVPscsi.device. Once it finds your drive, sismply partition it and format it. Then install 3.9. If you want more e help you can email me offline.
Steve