Active Directory issues

Hi there
I am project managing an Active Directory rollout. We have a number of large manufactring plants worldwide. One of these is a Windows 2000 AD domain, another a NT4 domain and another a workgroup. We are connected by VPN’s.
The AD domain is a mess with small workgroups everywhere. We wish to have a fresh start and as such a new AD 2003 Root server has been built in the NT domain with the view to migrate. Our internal DNS namespace will be different from external internet presence. Additionally we are using Notes/ Domino and there are no plans to change that. Does anybody here see any issues with this?