I know your pain my buddy, lol. First off the Phenom II even at 4.0ghz still holds back the HD7950 quite alot.
http://www.guru3d.com/articles_pages/far_cry_3_graphics_performance_review_benchmark,7.html
I personally have my X6 at 4.0ghz, with my North bridge overclocked to 2600mhz as well. I still have the same problems. Oh and my HD7950 is clocked at 1000mhz core and 1500mhz on the memory, but that doesn't seem to make any differance in Farcry 3. So I'm thinking it has to be a CPU bottleneck.
Basically I think that v-sync in the game is messed up, so the first thing you should do is force V-Sync(always on) through the CCC and turn on tripple buffering. Make sure that morphalogical filtering and surface format optimization are not checked while your in there as well.
In the game I set 1 frame thread lag(v-sync) to 1, and I also set pre-rendered frames to 1. Turn off AA alltogether, and you have to change the rest of the settings to a mix of High/very high. The only setting I highly recommend setting to medium is the water. I noticed the largest increase in FPS happened when I lowered the water to medium.
Hope some of this helps you till either a better driver, or new patch comes out to resolve the issues with stutter. It's a real pain when even fraps shows a good bit higher FPS than 30 but it stutters unless you can get the game to run at a solid 60 fps. I even tried editing the config file to cap the FPS lower and that did absolutely nothing.