Try downloading HDInstTools.lha from Aminet and see if it helps. The problem is most likely because of the drive being 5.1 GB and therefore it exceeds the 4 GB barrier of OS3.0/OS3.1.
If you got Kickstart 3.1 in the machine already, then try to get hold of OS3.5 or OS3.9 as the problems are fixed with these newer versions of Workbench (you will need the Boingbags for OS3.5 to fix the barrier problem though, but they are easy to find).
-EDIT-
Oh, I forgot. Try to just install the harddrive using HDToolbox. Ignore the - figure there might be. Go to the partitioning screen and set up some partitions. You should be able to create partitions without any problems, but will see strange figures when going past the 4 GB of the drive. Setup a 250 MB partition for Workbench, and install the OS. After that, find some patches (TD64) on Aminet and install them. You should now be able to use the rest of your drive.
Or you could just install SFS :-)