The disparity in university enrollment seems less troubling to me, since it is likely in no small part merely a symptom of a root cause somewhere in primary/secondary schooling or child rearing (which causes the high school graduation and literacy rate disparity).
Something during that birth-18 age range also seems at least partially responsible for gender disparities in major enrollment. Male:Female ratios for particular classes in CS departments seem to get worse as each year (a class that starts off 1:4 might drop down to 1:20 by senior year), but the fact that they start off bad suggests that something is going wrong earlier in the process, likely during highschool.
Identifying exactly what is going wrong in primary/secondary schools is paramount, but I see rather little to address it. There are many extracurricular programs designed to correct gender imbalances that appear during primary/secondary schooling, but those programs are addressing symptoms, not attempting to identify the cause. What exactly is it about highschools that make boys struggle with literacy more than girls? What exactly is it about highschools that set the stage for disparate university and program enrollment numbers?
If I had to venture a guess, without any sort of evidence, I would say that zero-tolerance policies probably affect teenage boys more than teenage girls, and therefore probably play a roll in teenage boys receiving a poorer quality education (particularly since punishments typically involve being removed from lectures... rather than receiving supplementary instruction.) Areas where self-education is viable and common, such as CS, may not be hit by this as hard.
Somewhat related to this article, there is greater participation in the workforce as well. So while there may be a wage gap among workers, it changes considerably when you include the greater number of men earning $0.
