@AmigaJules
At this point my friend, we need to start with the basics, especially if this is your first time setting up a >4GB Hard Disk Device.
Firstly we need to ensure that the Compact Flash Card is compatible with the Amiga IDE as some cards are firmware flashed as removable - which the Amiga IDE (in its native state) cannot use.
What kind of CF card do you have?
When booting your Amiga can you go into the early start menu and see any HDD/CF partition(s) available to boot from?
From your description its quite likely setpatch scsirom update is not being done in the start up, but let start from the beginning =).
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