In options I take it you have added your specified resolution, if not do that. Also, start the program before starting the game. And prior to starting the game, go here: c:\Users\(UserName)\Documents\Tilted Mill\Children of the Nile\
Open CotN.ini and find Full Screen Mode 1
and change that to 0. Basically you will be running in forced enlarged window mode but you will unfortunately see the border.
Change these as well to the resolution you want:
Game Window Height X
Game Window Width Y
You could experiment with this application
as well but I recall I got worse results than GWR.
There's a texture mod
you could check out too.
It seems I was wrong about the clipping issue at the bottom, you don't see the entire screen. This is how it looks like for me