In my opinion the best tool for extracting data in SQL server is SSIS, lots of flexibilty and good performance and has a lot of tools to help loading the DW. I don't really understand the whole "dupe" database scenario, why would you have copies of the main database let alone imperfect copies that you have to choose from?

If my requirement was to extract current data from the system I would consider an SSIS package that creates a snapshot of the main database and then pulls what I need from the snapshot. SSIS can BCP out to files or skip that step and have the data flow load it directly to the data warehouse.