I am not sure what exactly you are looking for. But, looking at the data, a linear one dimensional model does not fit so well. To see this, try CCA (Canonical Correlation Analysis): the linear version computes two linear transforms of the input spaces, such that the transformed data are maximally correlated. I suspect from your data that the maximum correlation you will get is no more that 0.7-0.8. If you are looking to "explain the data", you need a generative model, perhaps a Gaussian Mixture for good results.

For the practical aspects of data analysis, you can try *Handbook of Statistical Analysis and Data Mining Applications* by Nisbet, Elder, Miner. If you look to understand the theory, *The Elements of Statistical Learning* by Hastie, Tibshirani and Friedman is the standard graduate text (though it might be too difficult, if you are not at ease with probability, measure theory and functional analysis.)
Good luck!