While working on a show with minor clipping I was using the pencil tool to reshape the peaks where they flat-lined. After a few I was able to refine a method that produces good, consistent results. What I found works best (for accuracy, not speed) is to select one of the sample points (click and hold), and move your mouse straight up or down to place it; then, move your mouse straight left or right to the next sample and shift it straight up or down. An example of your movement would be up-right-up-right-down-right-down-right, or down-right-down-right-up-right-up-right if you were working left to right on the wave. Don't move your mouse in a curved motion. Many of you may have figured this out, but it really simplified my work and I thought it was worth sharing. Using a curved motion works, but can be a little more unpredictable. If you have a lot of clipping the curved method is probably best for speeds sake. With fewer clips this method provides more accuracy when manipulating the shape, in my opinion.
I've attached screen-shots of clipping on my file and how it turned out after using the above method.