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I have a January 2011 iMac with 16 GB of RAM and a SSD for my OS and applications, using a Pegasus 6 TB in RAID 5 conneced thru Thunderbolt for all the data.
Not exactly the same config you have, I know. I have no performence issues with my D800 files at all, and some get pretty large in PS.
Anyhow, a 390 MB file is not big at all IMHO.
I suspect, like Alan321 said, that you might have other processes running that are bringing your performance down. Just try the same thing with only PS and your Nik filter up and running and see how that goes.