i have to ask, how are your jumper configurations?
Since you sound like you have experience i am sure you checked this.
First thing i would do, is remove all add on card such as modem, nic, etc. So your saying you tried each hdd by themselves and same problem correct? By you saying that one drive doesn't show up in bios it sound like one is bad, or the two drives have a controller conflict. If the hdd's are good, then I would check the memory with a program called RST. Also, did you try a new cdrom, ide cable, on the hdd's and cdrom?
the two programs i use arw rst, and dft.
You need winimage to create the bootable floppies. Download and open winimage, open the dft, or rst file, then format and create each floppy.