How I do this.
Windows 98 is much more tolerant on reinstall than 2000 or XP which still use the primitive NT v4.0 installer which screws up most of the time.
If I do not suspect registry damage I'll try to install Win98 over the existing Win98 which will preserve the desktop, start menus and drivers. It it works, great, but if it doesn't fix the problem I have to reinstall fresh, but that still doesn't disturb the partitions or application data.
First boot on a floppy and log to the disk. make a \\WIN98 subdirectory and copy to it all the files in the \\WIN98 subdirectory of your CD, but not any of the subdirectories attached - they're all junk.
Log into the Win98 subdirectory and type SETUP. Leave the boot floppy in until told to remove it. Just walk through the install process step by step.
If I think the registry is blown, I rename user.dat and system.dat to user.rat and system.rat and do the install as above, but then have to install the drivers and major applications. In this case you will need a valid license code. In this case all your applications and their data are still on the disk but the programs won't run (MS Office, for instance) because their registry information is gone. Just reinstall.
If the thing is totally uncooperative I'll rename the Windows directory to Zindows and all the files in it starting with "WIN" to "ZIN" and install into a fresh Windows subdirectory.
After everything is working I can copy selected stuff from the Zindows structure to the Windows structure to recover some stuff (desktop, Start menus, address book, fonts, etc.). If I need to get programs to run that aren't reloadable I'll copy everything from the old Windows directory and \\Windows\\System directory that is not already in the new directories.
In a few cases I've had to rename the "Programs Files" subdirectory and let the install build a new one just to get Windows to boot, then transfer program subdirectories to the new "Program Files" directory one by one until I find the one that prevents Windows from booting (though most of the time I never do find what caused the problem).
If you can't find a CD with the exact version of Windows on your machine, you may have to remove the file WIN.COM (regardless of the directory it's in), and you will need a valid license code for the version you are using. It may also ignore the old registries in this case.
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