@jakes I don't really use k means (other than as learned on some online courses). However, I think you just want to transform your data to polar co-ordinated: a) A scale factor on the length, and b) Distance metric to allow for identity between $\pi$ and $-\pi$ (or $0$ and $2\pi$, depends on your conversion)
There doesn't seem much point in keeping x,y pairs in the distance metric that you are aiming for. Although if you want to explore different metrics, you could always include them weighted
