Terry,
As Bob said, some of us have it worse, or different but similar to yours. I am including a photo that I took of our '06 Endeavor that shows "ridges" across the motorhome. While this is not sagging like yours is, the fault with this coach was the thin sheets of luan underneath that separated from the supporting metal frame and bend upwards over time where the luan sheets meet. Bad adhesive job? I have identified 4 of these on my coach and a previous Monaco owner, by the tag of "Flyer" had a similar problem and went back to Harrisburg, Oregon to have it repaired under warranty. They replaced the roof but it appeared shortly afterwards! Apparently he was told by Kay Toolson that it did not need to be replaced and that it was normal. 13 years after we have owned this coach the raised ridges are still there, they have not gotten appreciably worse and there are no leaks. Normal? I don't think so, but I do not think it is a major problem as the filon has enough flex to withstand the upwards bending of the luan sheets underneath them. I routinely inspect them for micro tears but have not seen any since we have owned the rig. I try to avoid walking on them when up there but I occasionally do step on them without damage. Again, this may be different than your sunken parts. As well, the gap you are feeling on the sides of the roof is normal as the roof is one piece and "floats" on top of the frame trusses with nothing but the appliance covers and the weight of them holding them down. They are secured to the metal sidewall frames with screws, that do happen to rust, but the soft feel is normal when pressing down with your hand on the part that laps over each side of the motorhome. The front and rear caps are separate pieces the are sealed with eternabond tape to the one piece roof.