xchangx, it appears you don't understand some of what's been told you so far. A bootdisk with cdrom support will get you into dos, yes, but, it will allow the cdrom to run. The windows 98 CD will run from Dos. In other words, you certainly can reinstall from DOS. That's how the majority of Windows 98 installations are done in the first place. Comprendo?
If you go to bootdisk.com, download the file for Win98SE. Have a clean, formatted floppy ready. Run the file you downloaded, and it will create a bootdisk with cdrom drivers on it so that when you boot to Dos, you'll be able to switch to your cdrom drive and run setup.exe to reinstall windows. Make sure you reinstall it in the same directory it's in now (c:\windows) so it will keep all your current settings. Reinstalling that way will not lose your settings.
If you can get into safe mode, it doesn't sound like a total reinstall is actually necessary, although it wouldn't hurt anything. Exactly what version of Windows 98 are you using (first edition, or Windows 98 SE (second edition), AND, what files does it say it's missing? It sounds to me that you're really trying to say that you simply need to extract some missing files off the cd vs. completely reinstalling. If that's the case, what files does Windows say it's missing? Again, be specific about which version of Windows 98 you are using.