Scrap that, install went fine using WB3.1 instead of 3.9, Disk was seen correctly as NDOS and the WHDLoad installer picked it up just fine.
I was using just a plain Classic Workbench 68k with the Disk inserted prior to booting and the HDF set to a higher priority to the Floppy image to avoid booting from FDD.
I didn't need to update the installer or add any of the other bits discussed in this thread.
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