You have a reasonably capable machine (is similar to mine, just that I don't overclock), which should be able to run FSX. Why don't you try the FSX version ?
Stutters in FS9 are usually caused the the textures loading mechanism and, if a scenery has a lot of textures (don't forget that it's not "just" the JFK airport that need to be loaded, but also the whole surrounding scenery) since FS9 doesn't support the loading of terrain/texture with the 2nd core, your dual core CPU is wasted in FS9, when *loading* is concerned. FSX DOES load the terrain and texture with both cores, and this is particulary apparent with the reduction of stuttering.
Unfortunately, there's not much we can do, because the FS9 version is derived from the FSX version so, the scenery is designed to run at its best on FSX. Don't forget that, when you buy JFK, you are buying both versions...