@Will-i-am
I'm sorry to say it, but you must be doing something wrong when connecting the CD drive, because to my knowledge it's not possible that a CD drive that works on one Amiga doesn't work on a different one. I have swapped more than 10 CD drives from one Amiga to other without any problems, both from A4000 to A1200 and the other way around, even with a A600 all drives worked.
Are you sure that the interfaces are the same kind? AFAIK the A4000 Tower has a built in scsi interface, so if you are using this on the tower A4k, it won't work in the A4k desktop as it only has an IDE interface.
I'm just asking, because I have heard of people connecting a CD drive to their floppy cable, even though the socket and cable doesn't match. You should think that it would get people to think twice if they have done something wrong, but it didn't. Surprise, surprise, the motherboard broke.