If you've only had her for three days, your baby is likely going through relocation stress. This is perfectly normal, as she needs to get used to her new environment. As much as it's hard NOT to handle your baby at first - we all want to give plenty of cuddles and reassurances - it might be good to go "hands off" for a few days to a week to let her settle in well and good in her new tank. After she's settled into the routine, you can resume the handling you've started... in the evening is good. You can also continue to hand feed her, which is an excellent way to bond.
Don't be distressed that the little one runs from you when she's wide awake. Almost all babies go through that "ohmygodshe'sgonnaeatme" phase - and remember how very large you are to her! You just need to take it slow and easy, let her get used to the sound of your voice and your scent - two of the main ways your dragon will recognize you - and wait for her to grow up and settle down (you didn't say how old she was, but this could take some months). It sounds like you're off to a good start. Just remember to try to come at her from the side or front, not from above - that WOULD freak her out, as that's the direction a predator would come at her, and fear of things descending from above is hardwired into beardies.
Slow hand waving is fine. It's a submissive gesture, but doesn't mean she's scared of you. Rapid head-bobbing is dominance - trying to show another dragon who's boss. I've never seen a slow head bob, so I'll let someone else comment on that.
You'll probably be a bit stressed yourself as you and your dragon get accustomed to one another! This is an excellent forum for getting that stress resolved, as the folks here are very knowledgeable and happy to help. Take things day by day, and enjoy your new baby!
