I am assuming that you are asking how to transform multivariate time series data so you can analyze using PCA stated as on this wiki page Principal component analysis .
The analysis expects that the data are sampled from a P-dimensional random variable, and there are N samples. To the analysis, the order of samples does NOT matter, or in another word it does not care. In your example, it won't care stationary or not. Meanwhile, it won't stop you from supplying such data, in which the order of samples has a meaning. And it won't be irrelevant if one decides to ignore the order and look at the data from a different angle. Try throwing the raw data in and see what you may discover, or what inspiration you may get from the result. The main application of PCA is dimension reduction, e.g. reducing from P-dimensional data to a Q-dimensional data, where Q is much smaller than P. By that, you are already transforming your data to suit your needs, if that makes sense. In addition, you did not mention that you had tried differencing. Maybe you should try that and see whether that transformation means anything to you.