Well, I'm no expert in Amiga SCSI by a long shot, but I'd start with checking termination. I recall you said there as an accelerator in there but it had been removed, so things might be a little screwy. I'd check that your ribbon cable is hooked up something like this:
A2091 ---> Hard drive ---> CD drive.
Obviously check that pin 1 on the cable goes to pin 1 on the devices, then check the jumpers on those two devices. There should be one for termination on the hard drive and it should be off. There should be one on the CD drive and it should be on. In other words, you'll want to terminate the last device on the chain. So if your cable is going the other way around (i.e., connected to the CD drive first and then the hard drive) you'd terminate on the HD.
It gets a lot more complicated than that if you need to throw in active or passive terminators, etc., wait for someone with more knowledge to chime in if you need that kind of stuff.