First of all, let me thank everyone for your help and advice. I've come to the conclusion that Ellie is going through some old issues, moving pains, and puberty all at once.
Clipping is unnecessary for two reasons. One, in her flailing in the cage, she pretty much clipped herself (also, she got into too many nuts, and packed on a few grams. Nuts have been hidden, and diet adjusted), and two, she's more of a runner anyways.
It seems that (oddly enough) new situations are bringing us closer again, and the familiar is freak out zone. I think it's out of possessiveness and/or control. New places like outside, or the bird store she relies on me for comfort and protection (and a lot of the time she thinks it's the other way around). Familliar places are hers, and she seems to think i'm only picking her up to take her away from her stuff, and she doesn't like it. Especially her new crush, my roommate.
The best thing i've found to bring us back is honestly, not to care. Not to take things personally. I let her do what she wants (to a point) and reward her for being good (I.e. "If I don't freak out, I get a peanut). Cool Dad is making progress.
The final selling point happened today, when I took her to the bird store with my roomate. She was being kind of a braticus, cuz she likes the store, and it's getting to be familliar to her, and roomie was there. Well, there was a young male GWM there that took offense to her presence and wanted to establish green winged dominance. Ellie was holding her own and being relatively timid, but the action was getting too much for my comfort, so I tried to separate them. They were still just kind of yelling and posturing at each other, but the GWM made a move at me. I thought nothing of it, but Ellie took great offense and the GWM hade a facefull of Hawkhead. She took him to the ground and chased after him, biting and clawing, till I caught her at which point she snuggled close to my neck and kept looking around for anyone else who wanted to mess with Daddy.


p.s. she came willingly...actually, she gave me no choice but to give her a good scritchin cuddle fest on the way home. She may not always like me right now, but we're definitely family.