To bring this thread to its full conclusion I finally got round to modifying my copy of Gloom Deluxe.
I made an HD floppy disk image file and used Workbench to copy the contents of both disks to this file. I then modified the s/startup-sequence file to boot straight into the game without loading the setup program. I used ED from the AmigaDOS Shell to do this.
I now have a single disk version of Gloom Deluxe that works perfectly.