Nice! There really should be some kind of documentation, tutorial or example on how configure cards with isa_bios. Or better yet some kind of GUI application but for now it's a just the configuration file and looking at the perhaps a bit cryptic log file.
I was thinking about the IDE port. Are there rigid pcb's available that acts like a cable or would it make sense to make such a small adapter-thingy? Basically to mount the CF adapter right onto the motherboard without a flexible cable in between.
The Amiga people seem to have a few of these but the ones I saw were all putting the other end at right-angle which is less than ideal for space reasons.
I didn't think of it much since I always had it in my mind to cable to the CF adapter on PCI bracket, though I temporarily used this hackjob before the motherboard was cased:

