Welcome to the forums, Garry!
I'm sorry you are having problems with your budgie. The fact that she was running up and down the perch does not mean she wanted to lay eggs, she was just letting out her energy and being happy. Budgies do this when very excited and when wanting to get out of the cage for some flight time.
And yes, getting her nest box does potentiate and increases aggression on some female budgies. If they have latent bad temper, adding a nesting spot will increase the bad temper and violence/aggression.
Do not ever give her anything that she can use for a nest. Right now, she needs to get out of the violent frame of mind and that takes time.
You can rearrange her cage, do a total makeover in order to decrease her aggressive territorial behaviour.
If she does end up laying an egg, let her do so on the bottom of the cage, do not give her any nesting materials. By rearranging the cage or moving her to a completely different cage, you will throw her off the breeding/laying mood, and her laying cycle will be broken making her to not lay a full clutch of eggs.
Go back to basics as far as training goes, you need to re-establish a trusting bond with your budgie girl before attempting to have a more hands on approach with her. Start by talking to her on a calm, positive and encouraging way. Try not to show fear, because budgies are able to pick on our emotions and act according to them.
Only when you see her getting more curious toward you and actually moving closer when you sit by her cage, can you slowly introduce your hand to her and proceed to go through with the step up command (stepping up to finger or hand).
For more info and tips on how to improve the bond with your budgie and to train her, be sure to check the stickies on the Training and Bonding section of the forums.
I'm wishing you the best of luck with your budgie girl.