My FFT code FINALLY WORKS. It is pretty accurate (within 5 Hz usually) and works with my ukulele, and so I've started working on the code that tunes the instrument based on the frequency. I'm using a microphone that doesn't have automatic gain, so that definitely helps. So far, it's working pretty well (it tunes G especially nicely), but the unsteadiness of the output is messing things up. I can attribute that to the fact that the voltage doesn't vary that much, so the signal isn't the easiest to work with. To combat this I have to take the average of the output, which slows things down a bit but definitely makes it more accurate. If I can't fix this even more via my code I'll have to try and mess with the gain to amplify the signal some more.

Now, I am tweaking my code and microphone since the results are not as constant as I'd like.