The waviness of the skin, and twist that you showed in your first photos is totally normal for an assembly that has a skin that has been been rolled and press formed like the aileron nose skins have.
Twist related alignment in an assembly becomes locked in when the "box" is closed.
In the context of this assembly, that will be when the riveting on the spar gets done (that will be closing the box on the nose section of the aileron).
So to minimize the likelihood of twist in the aileron, you need to assure it is flat and twist free while the top and bottom flanges of the spar are riveted.
Opinions, information and comments are my own unless stated otherwise. They do not necessarily represent the direction/opinions of my employer.
Van's Aircraft Engineering Prototype Shop Manager
RV-6A (aka "Junkyard Special ")