What I have done is:
Formatted the A1200 and installed with OS 3.1
Installed IdeFix Express
Created an Emergency Disk with the CD 0S 3.9
Now copy atapi.device from from OS3.1/devs to df0:devs.
Installed the OS 3.9
Now copy atapi.device from from df0:devs to OS3.9/devs.
Stop here. Do not edit anything. Do not read anything. (Actually you may read the FAQ, but you should not execute any tip of which you don't understand *why* they suggest it and what it does).
Your problem is that you use a 4-way adapter on your IDE bus and the FAQ tells you how to get rid of IDEfix if you *don't* use a 4-way adapter. OS 3.9 does not support 4-way adapters by itself. You *need* IDEfix (or part of it, namely atapi.device) to drive the adapter.
The unit number tells it all. A "normal" IDE bus only has two units: 0 = master and 1 = slave. Your CD drive is at unit 2, so you have a 4-way adapter which has four units: 0 = primary master, 1 = primary slave, 2 = secondary master, 3 = secondary slave. But units 2 and 3 are only accessible through the IDEfix software, either atapi.device or scsi.device patched by IDEfix or LoadIDE.
Be,
Thomas