That's an interesting problem, because typically in Win98 Safe Mode you don't have access to your CD-Drives, and they are not listed.
Here are a couple of things you can check -
First, go into device manager and look under "resouces". The secondary and primary IDE controllers use IRQ 15 and 14 respectively. See if something else is trying to use those same IRQs
Next, look in the computer BIOS. On most PCs you get into this by hitting the DELETE key on boot up. Make sure both Primary & secondary IDE controller are enabled. Then check the main screen to see that it does not think that a hard drive is supposed to be occupying the controller - it should say "CD-ROM" or "None"
Next, open the PC up and make sure your power & IDE cables are still connected and tight.
Finally, use the utility in Win98 to make a Windows startup floppy disk. Once finished try booting up your PC from it. If you can boot from the floppy, your hardware is OK, its a windows problem.
If all these things don't change anything, you might want to try a Win98 re-install. You should be able to install over the top of what you have and not lose anything. Use your Startup floppy to boot the PC, then copy the entire WIN98 folder from the CD to your C: drive. Then go into that WIN98 folder on your C: drive and run Setup.
Hope this helps...