|"the IDE cable is a 40 wire cable"|
As I have already pointed out, all desktop IDE connectors have 40 or 39 pin holes, but the cable can have 40 or 80 wires.
If it has a blue connector on one end, it's an 80 wire cable!
You should NOT use a 40 wire cable if your DVD drive is a DVD combo drive capable of DVD-R and DVD+R 16X or greater, because it requires an 80 wire cable because it is capable of UMDA 66 burst speeds. The drives would still be recognized, but such a DVD drive would be unable to run any faster than UDMA 33 burst speeds when connected to a 40 wire cable - your burning software may not recognize it properly, and it certainly won't be able to burn at the drive's faster speeds without producing a lot of data errors.
A 40 wire cable is fine for all older slower optical drives - if the CDrom is by itself on a data cable, it will work fine.
If there's nothing wrong with the IDE cable, the bios settings, you have had the computer unplugged at all times when you were fiddling with the drive's connections, and you have the power connectors connected to the optical drives, the most likely thing is you STILL don't have the jumpers on them right, OR the new DVD drive is defective (if one is defective sometimes both drives on the same data cable are not recognized).
Different models or different makes don't necessarly have the jumpers in the same positions - check that again - or set them both to cable select. On optical drives there are often letters above the pin positions but they may be inscribed into black plastic and hard to make out unless you use good lighting. e.g. MA, SL (slave) , CS (cable select, that's not slave)
If that doesn't help, connect one drive at a time, as master, or as cable select on the end connector opposite the blue connector end (the blue connector must plug into the mboard) or on the end connector if it IS a 40 wire cable.
If you really do have a 40 wire cable (it doesn't have a blue connector on end end unless all of them are blue) it doesn't matter which end connector plugs into the mboard, but one end is farther from the middle connector and that's the one that should go to the mboard if the drives are fairly close together.
"I've read a few threads and saw to delete data out of the registry, but i do not see a upper and lower filter, ..."
In that case you DO see the drive in Device Manager, but it's flagged as not working properly - a yellow ? or a red circle with an black X in it.