Can't help with the device ID thing, but I've made another discovery:
To see if the IDE bus can actually support two devices, and to rule out board issues, I connected two ATAPI CD drives to it as master and slave, and booted off floppy. The Find Device list for atapi.device shows both drives properly, with master as device ID 0, and slave as ID 1.
This all seems to point to the CF adaptor as the source of the issues. I'll see if I can find a normal mechanical 2.5" HDD, and see if it works any better.