You can do a bit of magic alright.
Make your old W2k-drive the master again, and your new one the slave.
Then boot into your old W2K (which presumably was originally the C-drive), copy all the directories of a particular program over to the exact same location on your new disk (where again presumably W2K is on the C-drive).
Anyway, the drive-letter of the old programs must match the drive-letter of the new W2K-installation.
If you know which files from the e.g. Windows\system32 dir belong to this program, copy them also to the corresponding dir on your new HD.
You may find other relevant info in the uninstall-file of that program (if it exists).
Also copy the relevant data from Documents and Settings\ {username} \Start Menu to your new HD.
Then, if you are a bit of a registry-guru, export all the registry-data that you can find of that particular program, and put it all together in a temporary directory of your new HD.
Now reverse the HD's again so that you can start again in your new W2K.
Make a full backup of your registry, then import the program reg-entries from your old program (which you saved, see above).
Finally, try the new program to see if it runs. If it misses any files, it will tell you. Just copy them over from your old HD.
I realize this is the long way around, but if you dont have the original disks anymore, it may be your best shot.
There used to be a program-copy-utility that came with earlier versions of Drive-Image, but I can't remember the name (Drive-Copy?)