Steve,
Are you still using two monitors? This will probably have some impact although I have never tried it.
Also If you go in to the Display settings on FS2004, Go to the scenery tab and set the global scenery to "Minimal" then go to the aircraft tab and set the global aircraft quality to minimal and do the same for the weather. Then go to the Hardware Tab and make sure you Hardware is identified correctly turn off Render to texture, Transform and lighting, Anti Aliasing and Filtering. If this improves your frame rates start turning up the settings one by one till you get an acceptable level of performance and quality of graphics.
Hope this helps,