I am not sure what you are talking about, but it sounds like the typical Ford "clear coat delamination".
The clear coat begins to oxidize, and peel like dry skin after a sunburn. This will cause splotching, fading, and low spots in the paint.
the only other thing I can think of is, does your hood still have the heat blanket attached to the underside? Your engine heat may be affecting the hood composite material(fiberglass) and/or the hood has been repaired/repainted at a body shop by a previous owner.
Something to consider while addressing your hood. It is made of fiberglass/resin composite(to save weight) on 93-96 models, and aluminum on 97-98 models.