I told you, look in the shipyard. The game is hopelessly CPU bottlenecked.
I've finished the game three times with different hardware, and at no time did I observe any CPU bottleneck. In every low FPS situation that I came across, if I reduced AA or resolution settings, my performance went up dramatically.
Additionally, I carried out numerous tests back in the day, and changing the shader setting clearly showed it's the primary bottleneck, by far.
Dropping from high to low gains 115% (i.e. more than double the performance). The next closest setting is shadows which is about 35%, and the rest are lower than 20%, with many not even reaching double digits.
I can't imagine how you're not seeing this, being on stock Sandy Bridge like me.
Between the frametime graphs you posted and the artifacts you saw in UT3 and Fear 1, I think there's something seriously wrong with your setup.
I looked through numerous windows in Fear 1 and tried numerous the menus in UT3 with variable TrSS/SSAA levels, but I couldn't replicate any of your problems.
You said you had some CPU related tweaks in place too IIRC.
Actually they pretty much all reduce
GPU load (e.g. not running SSAO).
EDIT, not even in the shipyard and just look at it, 36fps with a single GTX 780 sitting at 60%, and you can see the problem CPU thread 100%:
Why does that screenshot look like you're flying through the air, and why is there no lighting (e.g. sunlight) being applied to any of the scene?