Sounds to me that the sensor of the floppy drive which recognises disk changes is dead or has a loose contact. Changing the floppy disk too fast (this is what the DOS thinks you are doing because of the damaged sensor) might confuse AmigaDOS so that it asks you to replace the CD although it is still in the drive.
I'd try to replace the floppy drive and/or cable or to try it without any floppy drive at all.
Might also be a virus or a loose contact somewhere else or a wrong jumper setting on the HDD or the CD-ROM drive or somewhere else. Quite difficult to decide with so much hardware in there. You should try a lone motherboard with one hardware component at a time (first the floppy drive alone, then the HDD alone and then the HDD + CD-ROM drive and so on).
Bye,
Thomas
