I know this is probably not what you want to hear, but... it sounds like you may have a Hard Drive that is on the verge of failure. So, the first thing to check is the drive.
Using your Windows 2000 install CD, access the Recovery Console command prompt. Here's a MS article that will guide you through the steps: http://support.microsoft.com/kb/229716 .
In order to boot using the CD, your BIOS will need to have the CD drive set as the first boot priority.
Insert a 2000 CD and boot up.
When asked, boot to the CD by hitting the Enter key.
At the "Welcome to Setup" screen, press F10, or press R to repair, and then press C (Windows 2000 only) to start the Windows Recovery Console.
Next, you will be asked which Windows installation to use. Hit the 1 key on your keyboard and then Enter (assuming that is the C drive).
You may be asked for an administrator password. At which point you will need to enter it or hit Enter if their is none.
At the resulting C:\Windows> prompt in the recovery console , type 'chkdsk /r' (with a space after chkdsk and without the quotes) and hit Enter.
This will start the scan and sector recovery.
Leave the computer on and undisturbed until completed. Be aware that this process will most likely take several hours to complete (sometimes overnight).
When it is done, you'll know if it is a HD failure issue or not.
If errors were found, run it again.
(chkdsk /r)
If errors were found on the volume and Chkdsk was unable to recover or repair them or if Chkdsk was unable to run at all, you will need to replace the HD.
If you do not have an external backup available, you will need to install 2000 and your other software on the new formatted HD.
Based on your post, it sounds like you may have to reinstall regardless.
To close the Recovery Console and reboot, type EXIT and hit Enter.
Here is another good reference for using the Recovery Console: http://www.practicalpc.co.uk/computing/windows/win2krec5.htm .
Please let me know the outcome.