A useful tool I found for finding out what files every program uses and wether it finds it or not is called filemon. It can be downloaded from here
try a short flight in it and see how many files fs uses and how many it can find (even just starting fs 9 and it searches for hundreds maybe even thousands of files.
So the less aircraft and other addons you have the faster fs should load, but if your having any problem,s with fs then give this a go and it can help you find what files your missing.
Aparently fs also continues to search for files wether ort not they have been found so this might even improve performance of fs if used in conjunction with the fs cds to install your missing files.

