I've just updated HeroMachine 3 with support for three new sets of items, female versions with properly positioned and sized ears, eyebrows, and noses. Mouths and eyes already had such sets published, but until now you had to manually tinker with the others to get them to fit.
Let me know if you see any weirdness. Hopefully this will make it faster and easier to create your female characters.
As usual, you may need to clear your browser cache (note, do NOT clear Flash cookies or you'll lose your saves!) if the new options aren't immediately visible in the set selection drop down list.