Active Directory Headaches NT4 to 2003

Hi,
Anyone up for a challange?
I am upgrading a NT4.0 domain to Microsoft 2003 Active Directory.
Test Lab:
Site 1 - NT4 PDC, BDC, BDC for rollback, 2 2k workstations, 2 2k member servers.
Site 2 - NT4 BDC, 2k member server, 3 2k workstations
Site 3 - 2k member server
Wish to use AD integrated DNS. Doing split brain, but haven't even got to use that yet.

Scenerio: Upgrade NT4 PDC to server 2003. When DCPromo part of the upgrade begins it says my domain name kitara.org already exists. This is because the previous admins named our existing domain kitara.org instead of just kitara. (domain name changed to protect the innocent). To get around this, I shutdown all my BDCs on the LAN and change the default gateway so it can't see anything on the WAN. My DNS name must be kitara.org because I have a web and mail server with this domain name. After the upgrade is finished, I change the default gateway back and reboot my BDCs. All seems well. Workstations and 2k member server on LAN register in DNS dynamically

Problem 1.
Workstations and 2k member servers dynamically register in DNS like they should. Workstations and member servers in WAN do not. Verified IP stack. All is correct, pingable, etc.

Problem 2
Site 2 member server lost trust relationship. Had to unjoin and rejoin domain. I am guessing this is because of the funky way I created AD in the first place?? Anyways, unjoin, rejoin, all is well. Promote member server to DC, all is well. Create DNS, not so well. Event logs show that there is a problem with Active directory. replication between the sites seems to be working though. Any clue? I can't create a forward lookup zone. Just trying to do a stub zone. No way works though.

Problem 3
Every test I do provides a different result. Trust relationships are the biggest. Perhaps my biggest problem is with the domain name itself. Has anyone had a domain name similar to mine with the suffix already appended and had to upgrade it to AD?? Am I just screwed?

I appreciate any feedback or advice you may have.

Thank you!!!