If FreeNAS is the OS, for what I need I can dump WHS once I get the data copied over.So I don't know the reason you would need the WHS after the data has been copied over. That's a decision you have to make, but personally I prefer to have all my storage in one box rather than spread out among servers. Been there done that. It was a pain in the arse.
To be clear you will need WHS on the server long enough to get the data transferred over the network to the new storage server.
How would FreeNAS handle the additional 2 Norco 42xx cases as they populate with data, do I just add them to the NAS pool?