The Windows Server 2008 R2 Active Directory Certificate Service Migration Guide is now available at http://technet.microsoft.com/en-us/library/ee126170(WS.10).aspx.
The guide describes the necessary steps for a successful migration of both enterprise and standalone CAs to Windows Server 2008 R2 from
Windows Server 2003 SP2
Windows Server 2003 R2
Windows Server 2008
Windows Server 2008 R2
and includes also the steps for migration to Server Core.