The 4gb barrier has to do with two things: the device driver (e.g., scsi.device) and the filesystem (e.g., FastFileSystem). Well, three things: also the hard drive prep utility's ability to understand the higher capacities as well.
3.9 fixes all of these, but I don't know if it fixes gvpscsi.device (it might). So it's easiest to prep a drive under 3.9. It can be done under 3.1 but it's more complicated, since all three components will need to be patched/substituted manually. An easy way to get access to the 3.9 tools is to use the 3.9 installer to create an emergency disk and then boot from that. No installation required!