Imagine for a moment that each program and piece of hardware is an expensive crystal glass. Imagine also that an operating system is a huge, wool and down comforter.
Now, when your system was intially installed your retailer laid the comforter (OS) on the ground and stacked each glass on top of it. What you have just done is ripped the comforter out from under the glasses and thrown it on top of them. As you can picture, this is not something you would want to do.
This is what I would recommend. If you can still get into the system, even briefly, make a backup of all important files (NOT PROGRAMS, unless you do NOT have them on CD somewhere.) Then I would boot to a floppy, preferably a Win2000 boot disk, and do the following:1. Delete all hard disk partitions through FDISK command. (Remember you have to delete a logical partition before deleting an extended DOS partition.)
2. Exit from FDISK and type "FDISK /MBR" (no quotes.) This will reformat your Master Boot Record to whatever operating system your boot disk is.
3. After that is done, you can reboot to the floppy and format the harddrives again.
Basically the above will allow you to build up on the Windows 2000 format. Remember that Windows 98 is FAT 32 and Windows 2000 is NTFS. This may be where your errors are comming in, even though Microsoft says Windows 2000 will support FAT32 harddrives.