You should keep petting her, that is a good sign that she is comfortable with her. And waiting until she head-butts your hand is the right approach. The shelter's 2-week policy may be why she is so timid, getting returned multiple times, and not having a chance to adjust on her own timetable. It's good that you made her a couple more hide-spots! Maybe put a few crunchies in them to lure her out - and that way you'll be able to tell if she's been in them when you're not home!

Have you tried any toys with her to lure her out? How about toys with catnip in them?