The 80 wire cable is preferred, and is required for cable select.
the 80-wire and 40-wire conductor cables have exactly the same signal pins. the 80 wire variety has ground pins to even out signal jitter and so forth. It doesn't add any features aside from that.
Cable Select works fine with a 40-wire conductor cable.
The 40G should be on the middle connector...other than that fine.
I Disagree. From what I understand of the semantics the 40GB is on one IDE channel/Cable at the end connector and set to slave, and the Optical drive is on a 40-wire cable anbd set to master.
Now, the problem is that the ATA-5... (or is it 6.... whichever one introduced ATA-133) is rather clear on a limitation that a cable should not have a Slave drive with no master; results can be unpredictable.
Therefore my suggestion is to simply set the 40GB to master, and keep it connected to the end connector of the cable.
Regarding the original issue that absolutely nobody has addressed at all-
Firstly, I noticed in IDE ATA/ATAPI Controllers in Device Manager list:
*PRIMARY IDE CHANNEL
*PRIMARY IDE CHANNEL
*SECONDARY IDE CHANNEL
*SECONDARY IDE CHANNEL
*STANDARD DUAL CHANNEL PCI IDE CONTROLLER
*VIA BUS MASTER IDE CONTROLLER
Why do I have 2 of primary and secondary IDE channels? Should I disable 1 of each?
One thing you can do is remove all of those, and reboot after you've removed them all. Windows should add only what you actually have. But, if the computer is working fine, you have no reason to change it. having a device ghosted in Device manager doesn't mean your PC is posessed or that it's going to explode or transmutate into a likeness of Jaleel White; unless you are having issues specifically related to the ghosted devices it's usually best to just leave it alone.