I've never chimed in before (here in the forums), but reading your process with the stuttering is so parallel with my experience I had to try and contribute. Sorry for the long post!!!
I have a high end system (X79, 4820K, SLI GTX780 (3GB), 16GB RAM, SSD, etc, running ENB as well) and I get the same problem. I've tried everything, spent hours upon hours researching this, and have come to the following conclusions:
It is worth distinguishing between micro-stutter and MACRO-stutter (a term I picked up on S.T.E.P). Micro-stutter is what you get when your system is producing too many frames, and the rendered scene exhibits very fast visual jitter (the whole screen vibrating - easily fixxed with an FPS cap of 59-60), and might also be accompanied by craziness in Skyrim's havok system. I believe the stutter you are referring to is MACRO, and is far worse with its intermittent delays and stuttering.
It has been my experience that when my system is tapped, meaning game/mod resources cannot flow freely between GPU/CPU and Skyrim, I get macrostutter when crossing cell boundaries, turning around suddenly, etc. It seems to last varying amounts of time based on the following variables:
(You didn't mention this but) Screen resolution has a huge impact. I'm running at 2560x1440, and all the texture heavy mods (including my own Lunari Race and Dragon Tree Temple), plus HD texture packs and Verdant grass mod, PLUS running ENB on top of it, that it maxes out my systems ability (dependent on Skyrim's engine of course) to move assets around smoothly. If I run my monitor at 1920x1080 I have zero macrostutter.
Shadow distance and detail seems to significantly impact my system as well. If I run fShadowDistance at 4000 I get stutter and decreased FPS overall. If I run fShadowDistance at 2600 the stutter is greatly reduced (playable).
Shadow resolution also makes a HUGE difference. There have obviously been so many community hours dedicated to deciphering and understanding Skyrim's mediocre shadow rendering system, and I have fiddled with it for far too long as well. Running ENB, I have set iShadowMapResolutionSecondary=1024 (farther shadow resolution), iShadowMapResolutionPrimary=2048 (intermediate distance shadow resolution), with iShadowMapResolution=4096 (closest shadows).
The difference between 4096 and 2048 for iShadowMapResolution makes a HUGE difference in macrostutter on my system. At 4096 I have some short stutters, depending on what resources need to load and how complex my location is regarding proximity to multiple cell boundaries. It's playable, but at 2048 I have virtually no stutter. I am using ENB of course, and so the shadows are GREATLY enhanced by the ENB detailed shadows function.
And there's anti-aliasing. I found when running ENB that it's best to turn off all four of the ENB AA options, and just use the SMAA function of SweetFx. I get a noticeable FPS jump when not combining the two. I am sometimes tempted to just run SweetFx, but after having spent some quality time looking at a well set up ENB, especially with ambient occlusion, detailed shadows, and bloom, I don't think I can go back.
I have had more problems than remedies with INI settings designed to support multithreading etc. I've tried it all, and honestly my system runs better without such tweaks (and I LOVE to freaking TWEAK).
In the end I find what you have already described - that with a heavily modded Skyrim, especially when those mods include masses of enhanced and HD textures, we are pushing Skyrim to the breaking point, far beyond anything it was ever designed for. Modding for me is so much fun, and truth be told, I am one of those geeks who spends far more time modding and checking out the inner world of Skyrim than actually playing the game!
I think it's fun, and often frustrating, to watch a game like Skyrim (and Oblivion before it) have such a long life as the community and the many brilliant modders out there pour their passion into the game to raise it constantly to the level we all want to see...
Let us know if you find anything else that helps with your stuttering...