Such configuration won't work, you can't share Simobjects folders between P3D and FSX, and our sceneries expect the Simobject are in the same flight sim folder as the scenery, and each and every sim.cfg of every Simobject has fallback paths that take this for granted. The pauses are caused by the program trying to create simobjects that don't exists or have missing files, because of this editing.
You should have said before you modified your .CFG file in such complex way, we would have saved lot of time, by simply saying such modifications are simply not supported, unless you know EXACTLY what you are doing but, we can't support you in such editing, and expect any scenery or GSX update will likely break any changes you might eventually have to do to the simobjects, so you'll have to do everything from scratch again.