As seen in picture, one of the pieces of wood is sticking up. The top panels are secured by nails that go through the perpendicular supports. I tried hammer the top of this wood panel back into the nail with no success. Then I tried just hammer up the entire piece so I can remove this nail but the other nails that secure this piece to the perpendicular supports are not budging. The nails from the bottom are embedded to deep to try to pull out too. Any ideas?
The chances are you are not unwarping the board. You can try but its been there a while and will probably go back. I would hit the really high point with a planer, get it close to even then sand (for a while) this thing flat. Yes it will take some labor time but the alternative of trying to make this straight will take far longer and probably not work.
Get yourself some 2-1/2" by 5/16" lag screws and washers. Secure the high corner of that board, and the diagonally opposing corner.
You could also do the job with 2-1/2" deck screws, but you'd have to clamp the board down flat first. Otherwise, the first screw will lock the board into position, which may not be tight, and subsequent screws won't be able to move it further.