Use the automatically generated connection objects that are created by the KCC, unless a specific reason exists to hard-code replication pathways.
Ensure that all your sites listed in DNS contain the appropriate SRV records.
Ensure that the schema version has been upgraded to R2 levels before installing Windows Server 2003 R2 on any domain controllers.
Use the repadmin and replmon tools to troubleshoot and validate Active Directory replication.
Consider using IPv6 for environments consisting of Windows XP and Windows Server 2003 and other IPv6-compliant devices.
Use IPv6 tunneling mechanisms such as ISATAP and 6to4 to provide long-term compatibility between IPv4 and IPv6.
Install the AD client on down-level 95/98/NT client machines (or replace them) to ensure connection to the closest DC.
Don't turn off site link bridging unless you want to make your domain controller replication dependent on the explicit site links that you have established.