I just stumbled upon this thread...
I only read it briefly, because it's a lot of posts.
As far as I understand you want to read an MFM harddisk connected to a bridgeboard in an Amiga 2000. I also have this setup and an A1000 with A1060 too. Both working! The A2000 with a hardfile (IIRC) and the Sidecar with a Filecard (Controller with MFM HDD).
In the A2000 I even have got an ISA NIC and I can access the internet on the Amiga side using the Etherbridge software.
I have been fiddling a very long time to get the A1000/1060 setup working. And it was just because of the floppy drive AND the HDD were bad. As soon as I got replacements it started working nice. I only had to disable a lot of bad blocks on the replacement drive. I used a software tool to know which blocks. You do not need any drivers.
I also tried one of those ISA/XT/IDE cards you mention. Unfortunately it did not work in the A1060. It worked in a PC.
So, if you still have any questions on how to setup, I maybe helpful. There is also an expert on bridgeboards on the German a1k.org. We could contact him if needed as I understand German.
A video to see the A1000/A1060 booting:
https://www.youtube.com/watch?v=6PamfEkIbQURegards,
Leo