First I'd like to know if you are OC'ing your GPU. I don't think your GPU is holding back that Q9550 from its full potiential.
Check this link out.
http://www.tomshardware.com/charts/gaming-graphics-charts-q3-2008/Microsoft-Flight-Simulator-X-SP2,783.html
You will see that my GPU is ONLY 1.40 FPS faster than yours! I do not know what set up Toms used to post these FPS but I would assume that it was the same for all GPUs and what it really shows is what cards work well with this game. That is why I bought the 8800GTS 512 then OC'd the #$&&%# out of it.
Since we both have the same CPU and 4G of ram the difference must be either an unstble CPU OC, OR you need to OC your GPU, OR a combination of both. Of course, lowering you settings in the right area helps a lot too. BUT you need to OC that GPU Spitefire7!
You have your CPU OC'd to 4GHZ, higher than my 3.83GHZ, yet this game seems unplayable on your PC at certain settings. Don't get me wrong here, I'm not trying to badmouth you. ALL of MS Flight sims have been ahead of the then current hardware available at that time. This was the first time I acutally tried to play this game MAXED OUT! So I was just a little surprised at my results to say the least. Meaning it was better than I expected.
I ran my PC for just under 7 hours with Prime95 "STABLE". A lot of posters here would say 12 hours at minimum to declare a stable OC on your CPU.
I also am using Vista Home Pre. 64 Bit as my OP/SYS. Plays better than XP pro 32 Bit. I'll probably get flamed for that but thats okay, I know what works best for me. I'm just trying to help you to play this game as well as you can. One other thing that would impact your game play(just came to mind)is the sound card your using. I have this sound card;
http://www.newegg.com/Product/Product.aspx?Item=N82E16829102005 It really does help especailly if you happen to be using onbd sound.
I talked to a friend of mine who has 2 880GTs and he says they OC to ~725 core and ~2000 menory.
Remember this thou, if you have downloaded the lastest drivers from nVida you will not see a great improvement with just 1 GPU. My 2nd GPU takes over the PhysiX from the CPU with this game and allows the MAIN GPU to just do all the rendering and the CPU free from having to do the PhysiX calculations. That alone may be why my PC is able to play this game as well as it does. (Just thought of that)
Hope this helps.