Haven't tried turning off hyperthreading or adjusting the processor affinity, but in regards to stuttering I noticed the other day when I was recording the game with Fraps that it would run more smoothly.
Instead of the constant jerkiness when flying at low altitudes, the game would run smoothly for a few seconds then stutter a bit then run smooth again. It didn't stop the stuttering altogether and of course it wouldn't be practical to have to record gigabytes of data just to run the game more smoothly, but I thought it was an interesting effect.
I'd guess the increased smoothness might have something to do with Fraps making the game run at a more constant (albeit lower?) frame-rate. Others have suggested in the past a frame-rate limiter might reduce the stuttering, but beyond turning v-sync on (or recording with Fraps), I don't know how a more constant frame-rate could be set.
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