I got some time to fiddle with this game finally. I discovered that it doesn't need to thrash one CPU thread.
To make the game behave itself, start it up, then change the CPU affinity for FarCry4.exe in task manager (right-click the process). Just untick a core and press OK, then immediately change it back to use all cores. Bingo. For my i5 system, the game then utilises all cores much more evenly. So, this is <gasp> a bug.
This also means that high CPU core usage does not contribute to the stuttering, as far as I can tell. I spent a lot of time laboriously testing each graphics setting and it is definitely textures > medium that cause the stuttering on my system (780 Ti) and nothing else.
Further notes: The image-retention that occurs with SLI is not related to temporal anti-aliasing. It still presents if you have no anti-aliasing enabled.
Changes to page file or disabling page file does nothing to help the stuttering problem. I only have SSDs in my system, so for people considering moving the game from HDD to SSD, this will likely do nothing also.