:-? I hate to suggest the obvious, but since your previous experience is mostly with SCSI, it’s possible that you’ve missed the simple things. IDE devices need to be set as Master and Slave, with the CD-ROM set as Slave. Also, I’ve heard it said that sometimes the actual position of the devices on the ribbon cable has an effect. Haven’t experienced this myself, though.
Also, older hardware sometimes develops eccentricities as it ages. (Just like its owner!) I used to have a IDE HD that enjoyed being Slave, but couldn’t work as Master. I suspect one of the circuits needed only for Master mode had burned out, due to a bit of static, or something.
;-) Try running your bigger drive, which hasn’t worked yet, as a slave to the smaller one. If it will work as slave, but not as master, you may need to replace it, as you won’t be able to use it with the CD. IDE Drives are (relatively) cheap, these days. If you’re on a budget, try your local computer recycling center. They should have plenty of last year’s hard drives dirt cheap.
