tobob
Which mesh are you using? I know that using Rhumbafloppy's new world mesh can cause issues with the stock scenery because his mesh is far more accurate than the stock stuff MS through together. The stock air fields are quite often not even close to being where they should be, and when Rhumbafloppy's mesh is used and the land is put into the proper place, you end up with some runways out in the middle of the ocean.
Not sure if the stock scenery can be relocated or if it will have to be recreated to fit the new mesh. I am not a scenery person...I have managed to produce some so so airports using FSSC, but they are just basic GA airports that I used to do my GA flying before I got FS2004.
OBIO