Uggg, the dreaded twist. I fought this with my elevators and now that I am working on the ailerons I am paranoid about it. First I think you could probably leave it and suffer no real ill effects. We are probably in the domain of what you can live with. Remember, as Vans says, your building a tractor.
Did you build the work surface that Van's mentioned in the instructions?
Is the flap ok with respect to your work surface?
Did you set the end rivets yet?
If the thing is good with respect to the work surface (my elevator problem was) it will be hard to fix without redoing your work surface. There are a bunch of rivets to drill out. Keep in mind that if you drill them out perfectly, and then reassemble, you could very well have a warped part again as they may set the way they did originally.