Installing Windows 2000, is not the problem, the trouble will be with your Master Boot Record.
Here's what to do.
1. Make or somehow download a linux boot disk, preferably one designed for Fedora.
2. Install windows as you normally would, boot from the disk and enter the install screen just be sure to use your Windows 98 partition and not any of your linux partitions.
3. After satisfying yourself with Windows 2000, boot from the Fedora boot disk and enter Fedora. To reinstall GRUB, which likely got obliterated from your Master Boot Record (MBR), go to terminal and type
which will bring you into grub's command line. You need to do two things here 1. reinstall grub into your MBR and 2 direct it to your boot partition with something like (see footnote on this)
Then you should be good to go, and if you want Grub to say windows 2000 as opposed to windows 98, edit /boot/grub/grub.conf. That should be self explanatory.
Footnote: You have to use the root command for the partition you boot off, for the setup command, use the same harddrive location as for root, but drop the comma and the second number. Look around for an explanation of the naming system, and if you have trouble post your fstab (/etc/fstab) and we'll tell ya.