From my experience, modding FC only yields about 1-5 FPS and is usually not worth the effort. In general, the only real modding one can do is to disable the shader effects, or use the settings ED provides. The only real modding you should do, in my opinion, is custom textures and custom models.
As to your system, FC does not recognize dual cores, so your CPU speed is effectively halved.
Drop scenes to Medium, Haze to Advanced, up colour to 32 bit (many effects need this to operate properly, and modern graphics cards are optimised for 32 bit).
Running FC in a window is a performance hit, full screen is best.
The overcast Mod is fussy, and doesn't make much, if any, of a difference.
WHOAH!!! AA and AF OFF! OFF! OFF! Not suprised you are seeing so much stutter. AF to 2 AT MOST (THATS ALL). Ignore the advanced settings, you don't need them.
As to the rest, you will just have to wait for my magic wand to come back from the cleaners.
Hope it helps.