Provided you have the Win98 CD and a working CDROM drive its pretty easy and will take a couple of hours plus a bit of follow up tweaking. It would also help if you can find your motherboard driver CD. You may also need the Win98 drivers for any add-on devices or peripherals you have (e.g. LAN card, modem, scanner, etc.).
I think it would be a good idea to try and get Scandisk (with 'fix' and 'check' ticked) to run in Safe Mode before
you do this, because there's not much point in reinstalling the system if your hard drive is dying. It would also be better if you can burn a CD with anti-virus, anti-spyware and firewall software so you can install these before you connect to the internet.
Here's my recipe for installing Win98 (hopefully SE):
You will need a startup floppy - Go to Control Panel, Add/Remove programs and there is a tab for 'startup disk'. If you can't do that make one on another computer, they're not specific.
Then these are the steps I would recommend:
1. Boot from the startup floppy with CDROM support and at the A: prompt type "FORMAT C:" without the quotes. If you are sure answer "Y" to the warning.
2. Put the Win98 CD in the CDROM drive. Because of the way the startup disk boots this will most likely be your E: drive.
3. At the A: prompt type "C:" (no quotes) return, then "MKDIR WIN98" return. This should make a new directory on your hard drive called WIN98. Check this by typing "DIR".
4. At the C: prompt type "E:" then "DIR", you should see several directories listed including one called WIN98. If not you are on the wrong drive and you need to try different drive letters until you find your CDROM. When you see WIN98 type "CD WIN98" then "COPY *.* C:\WIN98". This will copy the contents of the Windows folder to your hard drive (which makes installation and future changes easier).
5. When the copy is done type "C:\" then "CD WIN98". Do a DIR to check there are files ending in CAB present. then remove the CD and type "Setup".
6. Now you are in the Windows 98 installation program and you follow the prompts.
7. When Win98 has finished install the motherboard/chipset drivers and the drivers for any onboard devices from the mobo CD and reboot.
8. Now install drivers for any additional cards or peripherals from their manufacturers CDs.
9. Install Anti-virus software, anti-spyware software and a firewall. Then you can setup your internet connection.
10. Install your applications, reboot and your done.