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FaaastPrep is horribly outdated software, I doubt it can see much bigger than 300-400MB drives.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?