First of all how many users are you talking? If you aren’t a consultant planning to do this many times, you could well be wasting your time and aadding confusion versus just doing the job right manually for as many as 50-100 users. You really have golden opportunity to reorganize logically. I know we actually found 10% of files (200 users) were orphaned and deletable.
When I say this I mean building the 2003 machine with the new AD, accounts, and file folders with permissions in advance of final file move day. Better yet do a non-production trial with select users and get everyone’s password input on 2003 accounts before the final file refresh for going production. I’d actually move NT4 files this way first then NDS files later to break up the effort required.