I've been driven quite mad by a weird kind of stutter that only happens when sprinting. The only working fix I've found is to use iFPSClamp which breaks game events as we now know. I suspect it's some kind of animation glitch/desync, it doesn't happen all the time but it seems to kick in after sprinting over long sections of more complicated geometry such as cracked roads and the pathways in Diamond City.
Using the console to enable no clipping immediately solves the stutter, I suspect because the character model isn't physically interacting with the game geometry. When no-clipped I can run (use godmode to sprint forever) around for as long as I like and not see any stuttering but as soon as I enable clipping it's only a matter of time until the stuttering kicks in.
It's as if the character animation gets desynced by colliding with certain types of geometry, maybe iFPSClamp forces everything to sync up and this is why it fixes the stutter yet breaks other things...I dunno, I'm no coder
It doesn't happen when walk/running, only when sprinting. If you're sensitive to these things and want to test for it - open the console and enable godmode (tgm) for infinite sprinting and run all around Diamond city for a minute or so (especially around the rear) and see if you can sense a juddering motion...it even slightly messes with the post process temporal anti-aliasing so the stutter is definitely affecting motion of the in game camera.
*edit*
I'm not 100% sure it affects the anti-aliasing, might just be seeing things because of the stutter.