Upgrading Active Directory to include a Windows 2008 R2 domain controller in an existing domain where the DC is 2003.

This can be a real challenge. Document the process  to get it right every time.

First check your 2003 DC with dcdiag.

Not included in the box, download the support tools:
http://www.microsoft.com/en-us/download/details.aspx?id=15326

Fix any problems before you begin. Note that failing the test SystemLog just
means there are failures in the System Log….

Next, prep the domain using the adprep tool, taken from the 2008 CD under Support\ADPrep. MAKE SURE YOU USE adprep32 on a Windows 2003 32 bit machine!!!

Run in this order:

adprep32 /forestPrep
adprep32 /domainPrep
adprep32 /domainPrep /gpprep
adprep32 /rodcPrep * not compulsory but must do if you plan to install a Read Only DC.

Now on your 2008 machine make sure the only DNS entry is pointing to the old server, this may change once you dcpromo.

Once this is all working you can check replication then move the FSMO roles.

Use the event log, Luke!

Tools:
dcdiag ( /q for errors only ; /v for verbose )
repadmin /showrepl – check replication
repadmin /replicate destinationdc sourcedc DC=domainname,DC=local – replicate now
ntfrsutl – check the file replication service.

References:
Petri 2008 ADPrep
Petri FSMO roles
Troubleshooting Netlogon and Sysvol transfers