I’m not exactly sure if I followed your description correctly, so let me see if I have this right:
You currently have a SQL2000 server running. You want to upgrade those databases to SQL2005 on a different box. And the issue you’re having is orphaned local Windows accounts after the upgrade.
First off, unless you have a method of copying the SAM and having that work on the new server with a different SID, you’ll need to do a full copy of the old server and restore onto the new server. That will bring over the local Windows accounts. Otherwise, I would suggest (if this is an option, since I don’t know your environment) making the local accounts domain accounts. The you can do a fresh build on the new server, install SQL2005, and migrate the accounts over.
Otherwise, you’ll have to build the new server, manually create all of the local accounts, install SQL2005, then migrate the databases over. I’m not terribly Windows savvy, but I’m not aware of any way to script the automation of copying the Windows accounts from one server to another.
I hope this helps.