Windows Server 2003 (R2) Active Directory Infrastructure Best Practices
Make sure that schema version has been upgraded to R2 levels before installing Windows Server 2003 R2 on any DC.
Make sure that all sites listed in DNS contain proper SRV (Service) records.
Use automatically generated connection objects, unless a specific reason exists to hard-code replication pathways.
To troubleshoot and validate AD replication use repadmin and replmon.
Don’t turn off site link bridging unless you want to make your DC replication dependent on the explicit site links that your created.