phase angle of harmonic
Your window is centered around the middle of the time window. This corresponds (roughly speaking) to a delay of half the window size and corresponding additional phase of $e^{-j \cdot \omega \cdot t}$

The "wiggles" that you see is a steep linear phase that wraps around 2*pi occasionally. There a few ways to fix this.


circularly shift the time domain signal so that the max of the window is at 0. This will be better but still isn't great since the windowing will significantly impact the phase. 
Make sure that the fundamental fits into your time window and integer amount of times. Then do an FFT without windowing. This should give you an exact result.