Are you positive the floppy drive controller on the mainboard is dead? The cable could be bad, connnected in reverse, or the floppy drive itself might need to be replaced. Floppy drives often become dirty and then refuse to identify a disk. In any case, I'd replace the cable and the drive and see if this corrects the problem. If not, then a new mainboard may be in order.
In the meantime, you should try to get access to another computer where you can connect the hard drives. For the primary drive that contained Win2K server, this should be jumpered and connected as a primary slave, and then a program like Partition Magic 7 from PowerQuest can be used to format the system partition. Or a downloadable disk utility from the manufacturer can be used to low level format the disk, after which, you can use FDISK or the utility to recreate the partition(s).
As for the slaved drive with Win98, all that may be necessary is for you to be able to use FDISK to make the system partition active so that it is bootable. Then the drive can be jumpered as the master. If Win98 is intact, this should allow you to reach the operating system GUI. If this isn't applicable, with access to another system with a working floppy drive, you'll at least be able to format the system partition in preparation for reinstalling an operating system.
Note: Be sure that when attempting to boot with a floppy drive and a <A HREF="http://www.mirrors.org/archived_software/www.bootdisk.com/original.htm" target="_new">boot disk</A> that this is selected as the first bootable device in the BIOS setup. It sounds to me like your first bootable device is CDROM, and this could be the source of the entire problem.
Toejam31
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