Stationary time series for clustering algorithms
Have you tried replacing the entire timeseries with some meta data of it - clustering on each point of a series seems to be a bit exzessive. Especially as then if your timeseries are not synchronized they might not be considered similar - eventhough they might be for the purpose of this exercise (Imagine two sinus curves but one is slightly phase shifted -- If you would want to cluster by frequency then these would be equal). 

So you could try to do something similar to Fourier transformations Fourier Transformations, linear fits, etc and use this meta data as input for the clustering.