Looks like the drive is ultra fussy, only connects on same bus with other HDs of the same close family, not any kind of ATAPI drive.
https://www.seagate.com/staticfiles/support/disc/iguides/ata/9144ig.pdfIt's from 1992.
It looks like MUI is expecting to be in Workbench:system drawer. Which is maybe where it is on your hard drive, not your cF card?
For some reason, your startup sequence is also loading up Aweb. Which isn't going to help getting iBrowse working. Probably it makes no difference.
But to me, looks like all of your problems boil down to your hard drive not being available, so everything is in a different place to what the system is expecting to startup from.
It does not help that CF adaptors are also fussy about sharing an AT channel.
A quickish but flawed workaround would be to make a new drawer on the CF card, copy all the current Workench partition to it (from the card, to the card).
Then turn off, disconnect the DVD-ROM, plug the CF card and HD into one channel each, boot from the CF, and copy all your HD boot partition straight to the boot partition on your CF card.
Turn off again, unplug the HD, and reconnect the DVD-ROM in the same place. Turn on, and your CF card should boot same as your hard drive used to.
BUT... if every time IDEFIX locks up whene the HD is connected (it can't speak ATAPI) then you really might have to use a separate controller to get the data from the HD to the CF card. Or perhaps upload it to the internet from your machine booted from just the HD, then downloaded onto your CF card.
The reason for the reboot is because you are using 3.1 ROMs, by the way. The system is upgrading components (like large drive file system), needs a reboot for them to take effect. Later ROMs (3.x and now 3.1.4) don't have that issue.