First things first, clone your hard drive to a 'spare' HDD of at least 2GByte larger than the total amount of data on the file system (say you have a 80G drive w. 32G of data on it; use at least a '33GB' or a 40GB drive). Your HDD manufacturer may have free tools to accomplish this. Before cloning, it never hurts (other than time-wise) to run a full read test of the drive (again with HDD manufacturer's tools) to verify the state of the drive. Beware that depending upon the cloning option(s) you chose, your clone might not be bootable.
VERIFY that your data was copied sucessfully (ubuntu's file manager may help).
Use your Windows2000SP4 (if you have SP4 on your system) to do a (R)epair of Windows 2000 from initial start-up (be sure your clone is disconnected FIRST).
Beware, i am not that well-schooled in the proper repair procedures for Win2K. The repair procedure might break your apps, screw-up a DOS partition if applicable, you may have to re-apply ALL windows updates (after SP4 - if that's what your working with), driver issues, etc, etc...
]
My gut feeling is that it might be possible to upgrade to WinXP-SP3, keep existing apps, use DOSBOX to emulate a DOS environment for your DOS proggies.
No matter what you attempt to repair your existing partition(s), you may have remnants of viral/malware products, or if parts of the OS/apps become broken by the repair processes, the result may mimic the affects of a virus/malware (in rare cases). Spybot Search&Destroy has been invaluable to me (they have a boot CD - not sure of price/availability). Malwarebytes AntiMalware is ok as well (no boot CD).
I'm not so much of a fan of Kapersky, since it puts a new folder in the root of your HDD. I'm not sure as of yet why (possibly for Quarantine, or to leave a copy of itself on your HDD to access later).
I have had a lot of success with Avira's rescue CD, though.
Ccleaner (from piriform) is a great tool to clean the registry, etc. http://www.piriform.com/ccleaner/faq/in … er-support
When 'yer done, here's some DOS goodies: http://anarethos.dyndns.org:8080/