Step 1: Stop using FaaastPrep.
Step 2: Use the latest version of HDtoolbox.
FaaastPrep is horribly outdated software, I doubt it can see much bigger than 300-400MB drives. You might be able to get it to work but you're just making it a lot harder on yourself by not using proper tools.
Also, I'd make sure you're on the latest ROM for the GVP and that your jumpers are correct on the replacement drive, while you're at it. 
Edit: sorry, haven't had enough coffee yet today. You're saying with the replacement drive installed and the autoboot jumper on, the system will not boot at all? Even from floppy?
Actually I quite like the later versions of FaaastPrep, I use FaaastPrep v2.0 for most of my pre AOS 3.5 and older installs. I never found hdtoolbox all that user friendly.
Further, I used it with the commodore brand scsi controllers as well as the scsi chip is the same that is use in gvp.
It can do luns change all the things you want like maxtransfer, priority and allows you to use other load versions of fast file system. I have not attempted to use pfs of sfs with it however.
It definitely beats any of those IVS or Dataflyer SCSI configuration programs.