Hi Genie,
Am afraid I'd go a bit back to front on this one... While Stoney's advice makes reasonable sense to us as humans, a rabbit is not human. They have a different 'socialisation' as such.
There is an old saying that you will never catch a rabbit if you chase it.
5 years of confinement is unlikely to be a negative thing by now. It is a familiar thing. A safe thing. I would always ensure the cage is open and accessable, at ground level when ever she's brought out. Actually, a door that permitted her to come out would be better than lifting her out. Allow her to move in and out of it and broaden her own comfort zone, so to speak. Just cos she goes in, doesn't necessarily mean she's finished being out. She may just need to know she can get 'home'.
If she is given regular time to free range, then there would be no need to get another house, either. Your home will become her extended cage.
Rabbits pair off, and a single rabbit will buddy up with a human. In a family situation the rabbit will choose its owner, and that isn't always the one who begged for it, cleans its cage or named it.
While confined in the petshop it is very likely the rabbit was handled by lots of people who did not know how to properly lift a rabbit, so contact may still be hindered by a fear of harm. It is very important that rabbits rear legs be supported when they are lifted, and this often doesn't happen with a child picks it up to cuddle it. They tend to lift and hold them under the front legs which puts huge pressure on their spine. They respond to this pain by scratching and attempting to get back to a horizontal position. The kindest way to hold a rabbit is in the crook of your arm, which encloses and supports its whole body. Remember they choose instinctively to live in warrens. Warrens are very confined spaces. Animals very quickly establish their own trust, and handling has a huge amount to do with this.
Lots of animals communicate with nips or bites, but rarely are they saying anything like what we go on about. They use their bodies to signal needs (and fear). A rabbits teeth need access to solids, to wear them down and maintain gum hygiene and digestion. Many pet rabbits are often just provided mixes that do not meet this need. They will nip and bite to communicate this need. Some may also head butt or rub their heads (mouths) against you. Try saying a sharp no when she nips, and calling her to follow you while you provide a suitable alternative (carrot, piece of bark, cabbage).
Toilet training will also be helped along if you watch for signals that will occur in the right body area
. Prior to letting go, she will enter a routine, which may be short, and might include a certain path she follows before skipping, sitting, squatting, tail wagging or shaking. Watch and you will see it.
I don't think your wee bunny is frightened of you Genie. I think she has quite likely been socialised to a life of constant change, new faces, poor handlers, poor conditions, and she just needs a bit of time to trust that you will be there each day and are willing to interpret her individual communications and meet her needs. I wouldn't keep changing things around her too much. Just hang in there and keep being reliable.
You know those polystyrene boxes that broccolli comes in? If you whack a few inches of soil in there and heavily sprinkle with a parrot mix and keep wet for a few weeks. Then cut a door in one side and leave it out for her. You will have regular boxes of brilliant green feed for her and she will just love getting in there and munching her way through it.
Make a sort of 'whoooorrrrrr-ooooorrrrr' sound. Well you know what I mean!!
