I have a Phenom II x4 and a HD 4890. Wow 16GB, thats alot. You have in 2x 8GB stickes, right? Two sticks of RAM, work together much faster than one by itself.
My last GPU was 9800 GT. So its not the CPU's or GPU's.
I fixed a similar problem in oblivion. There are so many objects in such a large area in Oblivion, that the hard drive is the only thing that has trouble keeping up with the rest of the system. I installed an SSD and put only Oblivion on it(no OS, just Oblivion), so great had become my obsession with ending the stutter.
That greatly decreased new area loading stutter. However there was some left. I read that the game graphics have to be in synch with the physics engine and if the physics engine is going faster than the onscreen graphics or vice versa there are missing frames(The frame yo-yo-ing you/we saw).
Go to "Tweak Guides" and enable all the multi threading options it lists in the .ini file. Not all the multi threading options are good, some can cause crashes like, "Multi ThreadingAudio".
Enter a new line in the .ini, under the "General" heading of it; "iNumHWThreads=6". This should tell the program there is 6 cores to work with, not sure though. Make sure that V synch is enabled. V synch is there so that your graphics card is putting out the same frequency/frames as the monitor you are using. I've heard people saying that it should be turned off to get maximum frames, but that is totally wrong. If you turn it off your GPU will burn itself out putting 8000 Frames Per Second on a menu screen and not only that it causes ugly screen tearing. See the stutter in itself is simply occuring because the difference between our highest frame count to our lowest frame count is so drastic that there is no gradual slow down in speed. Enabling triple buffering on ATI Catalyst Control center further smooths the frame difference further(not sure what Nvidia equivalent is).
And finally go to "iFPSClamp=" in the .ini and set it to either "=60"(for normal speed). If you want Skyrim/Oblivion the sonic go with "=40" and everything will be really fast yet smooth.