I'm going through something similar except I can't even get windows XP to come up on my computer.
I've got my old one hooked up to the internet now, and my 6 month old dell is out of commission till I can either figure out how to fix it or reinstall windows.
Not sure how this happened but it has been BAD! I'm trying to use some old files from windows restore to fix it but not having much success.
Good Luck. Same thing happened on my new Acer notebook computer. Had to use the restore dick and lost everything on the computer. Fortunately my other 'puter is Mac.
I reinstalled my Windows 98 once. It wasn't too difficult.
Also, when I get a message about a corrupted or missing file, I look to see which directory it belongs in and then start looking for it in my cab files, which are located at: C:\win98. I right click each cab file, click View, and look for the missing file within that cab. If it's not there, I go on to the next cab. It takes a few minutes to find the file. When I find it, I right click it and click Extract, making sure the I put it in the right directory.
Use cleanpar (Google it and should be able to find and download it) and wipe that sucker clean. Then......do a fresh install of XP. Been there, done that.......often.