You cannot run an MFM-drive on the ISA/IDE adapter. MFM is not the same as IDE. Even if they have the same connector.
Idea started as, Wally has lots of IDE and SCSI drives, but no controller to attach to Amiga.
With the IDE / ISA controller, he can practise setting up hard drives on Amiga and Bridgeboard, so can undestand better how the old school Oktagon is setup.
Plus, it gives him a place to store all the data he can access, once he can access it.
Wally, it was an honour to assist you. 99.99% of people do not want to know about the stone age XT systems and how tricky they were. I don't think drive has an Amiga bootblock as such - first parition is DOS, so should be where Bridgeboard can boot up from when Janus is running properly (needs to be cofigured properly). You personaly always started your system with booting from Amiga floppy on 1.2 system, so why need Amiga bootblock on hard disk?
Ribbon cables suck, long term. They wear out, get tatty and damaged, unreliable. I was taught at factory and lab, any sign of damage, replace. Cannot rely on damaged cables. Even a clumsy melt from contact with a soldering iron, I had to make up a fresh cable. Not acceptable to the end user (industrial, transport and military buyers).
Stick with Kickstart 1.2 system for getting your data. Then switch to 1.3, setup proper Amiga hard driveboot, and never worry again about floppy drive startup. (Until Amiga hard drive stops working, all hard drive with moving parts will wear out one day).