Put the following text in a script and run it from the compilation directory.
Code:
Assign <disk label>: ""
Assign Fonts: <disk label>:Fonts/ ADD
Assign Libs: <disk label>:Libs/ ADD
Assign S: <disk label>:S/ ADD
Assign C: <disk label>:C/ ADD
I don't know if you've tried this already, but if you haven't then you definitely want to.
And I'm assuming that when you were making your assigns that you used the label of the disc and not CD0:, otherwise you'll have some editing to do.
Also, seeing as the HD compilation is intended for users of an actual Amiga, LHA would be preferable to ZIP.