Dual-boot 98/2K, bad W98 needs fix or 96

I have a dual-boot Win98/Win2K machine that the Win98 is totally corrupted to the point that it will not recognize any new software or drivers you install. The drive is one partition, FAT32, with Win98se and Win2K (sp3)on it. I have tried to reinstall 98, however it still comes up bad. So my alternative would be to remove the 98 wihtout disturbing the W2K. They are installed in separate directories (Windows/Winnt). I’m looking for answers to both choices, Repair- How?
Remove- How?
Thanks,
K