Migrating from one SQL Server 2008 R2 instance to another
This should solve your problem: 

http://msdn.microsoft.com/en-us/library/ms345408.aspx

That link has instructions to move system databases from one instance to another, if you move all databases as is (including user ones, for which you can copy the file, however you will need downtime, or if your databases are on a SAN you can use a SAN snapshotting software), the SQL Server will come up with everything intact.. Keep in mind that if you have a named instaces (NAME1\NAME2) then the NAME2 should be same for the destination instance..