I have been working on an Android project for awhile that displays the fundamental frequency of an input signal (to act as a tuner). I have successfully implemented the Audi
I suspect that the strange results you're getting are because you might need to unpack the FFT. How this is done will depend on the library that you're using (see here for docs on how it's packed in GSL, for example). The packing may mean that the real and imaginary components are not in the positions in the array that you expect.
For your other questions about window size and resolution, if you're creating a tuner then I'd suggest trying a window size of about 20ms (eg 1024 samples at 44.1kHz). For a tuner you need quite high resolution, so you could try zero-padding by a factor of 8 or 16 which will give you a resolution of 3-6Hz.