As others have said, don't fin when the surge is coming at you head on, only when it is pushing from behind. That way your kick counts will be more accurate. Kick cycles, I have found, are most useful as an aid to swimming patterns for search and recovery. For ordinary diving, the navigation method I use most is definitely natural features, followed by compass headings (or a combination of features + headings). As doubler mentioned, I always tell students to look at the feature they are making note of from the opposite direction so that they can recognize it on the way back.
As far as feeling that you failed because you missed the mark by 30 feet while swimming the square, consider the real-world use of being able to navigate (regardless of the method) back to your starting point--it's not because that's what the book says to do; it's because that's where you left your boat or that's where your beach exit is. If you surface 30 feet from your boat, that's okay--it's close enough to swim to on the surface. And if you come up slightly down shore from your entry point, that may be okay too, since you won't swim straight up onto the sand like a beached whale, but instead you'll surface near the beach but far enough out that you can still do a little surface swim to get closer to the exact place you want to be. What you are trying to avoid is coming up so far from your boat or from your beach exit that you have a long, tiring surface swim to get to it.
So while you may feel that you have not passed with flying colors because you missed the mark or because your counts didn't work out perfectly, I believe you did deserve to pass, and in addition, that you learned a great deal from the experience, which is the main thing. I often think that students who nail the nav tasks perfectly the first try learn less than those who struggle a bit.