Place the Win 98SE boot floppy into your A drive and boot from it. When it boots, put your WIN 98SE CD-ROM into the drive and select install from CD-ROM. I'm not sure if Win 98SE offers a "repair existing installation" option, but if it does, select this rather than a full installation overwriting all old files. It might also be possible to just boot straight from the CD-ROM anyway. If so, do it.
I assume all your drives are already formatted. If this is the case, select the option "Do not allocate unallocated disk space" and allow the installation process to go through to completion.
Hope you backed up the really important stuff!
Once your OS is installed and the machine boots into it, get out your CD-ROMS with Windows updates, service packs etc and install them.
If you haven't got these on CD-ROM, then you'll need to download them from the Windows update website.
Make at least one Win 98SE boot floppy now, and put it somewhere safe!
Re-establish your internet access and make sure your anti-virus/spyware is activated. Log-in, download and install updates etc as required. I like to save the updates onto disk and install them later - that way I can archive them in case I need to do a full re-install.
Now restore all your important data files from whatever backup system you use. (I use the backup software once a week, but transfer changed files onto my notebook machine once a day).
At this stage you should be back to a reasonable Win 98SE system again. You may need to re-set your preferences for screen resolution, screen-savers etc.
98SE has a huge base of users (I really like it) but I am considering an upgrade to WIN 200 Pro, which I have on my notebook machine and which has been exceptionally stable. 98SE will be supported for only a few more years, according to Microsoft. Chances are you may be able to buy a full-install CD-ROM of Win 2000 Pro very cheaply. Worth considering.
Hope this helps. A clean install does get rid of a lot of junk that accumulates over the years.
I found I had to stop the installer from configuring unallocated disk space or else it failed to assign the CD drive as drive C and the installation aborted. This frustrated me for an hour or so. I have all SCSI drives in my system, perhaps the 98SE installer is really designed for IDE drives. I used FDISK to partition and format the drives before installing the OS. That may have upset the installer also.