If you are being limited by hard drive speed (which is implied by the question), you could try loading skyrim into a RAM drive. With 16GB you should be able to create a 10-12GB RAM drive. That would hold all of skyrim plus a number of very large texture packs. With that configuration I assume you are running SSD in raid? If not, get some as that would be by far your biggest limiting factor for performance in and out of Skyrim. If you are running a lot of textures you could also build your own BSA files which would speed up access over using loose files (improve load speed of textures, etc). This wouldn't be as important with a RAM drive, but would help with SSDs. You may be having problems with CPU rendered shadows in that configuration because Skyrim is known to not offload shadows to the GPU(s). You could try turning them down/off for an easy test/fix. One way to detect a CPU bottle neck would be to launch task manager, tell it to graph your cores individually and see if any of them are running near full speed. For reference, my configuration isn't as beefy as yours, but I'm completely CPU limited on an overclocked i7-920. Finally you could use Elys's meminfo (available here) to tell you how much ram you are actually using (and determine if it's your limiting factor).
