I don't think you can apply the same techniques, since they depend on a special property of the Y-chromosome and mitochondrial DNA: they are not affected by sexual reproduction, only by mutations.
Huh, you're right- studies on the altogether most recent human common ancestor are all based on pure statistics. I'd thought that genetic recombination could be accounted for, since its not as though genetic information (and the mutations therein) are being lost in the process, but apparently no one's found a way to do this yet. Interesting... ! :)