This all sounds very familiar! Alice was always very friendly to me when I went to visit her, but after the first night in the cage she was very reluctant to come back out unless it was to sit on top. It has gradually got better: just the occasional step onto my shoulder during the first week, then a little more regular, now if she hasn't seen me for a while she wants contact right away, and she splits her time 50/50 between the couch where I generally sit and the cage. I also put a couple of low perches on the outside of the cage that give her somewhere she can climb down to if she wants to be near me on her own terms, and she uses them a lot, and I'm hoping soon she'll be confident enough to get to the couch and back without me picking her up. I think if you let her set her own pace you'll start to see improvements soon enough, she just needs time to acclimatize to her new environment.
I'm not sure what to suggest in terms of getting her down from the top at bedtime. In my case she doesn't do the step up command (yet) but if I put my forefinger behind her feet and my thumb in front whatever she's doing she'll automatically lift up her feet so that she's standing on my hand. I don't think she particularly likes this tactic so I save it for when I absolutely have to pick her up - and I'd be very nervous of pulling that trick on a bird that might bite, but Alice is a *****cat in that respect. She also hates bedtime, but she usually saves her tantrum to when the cage is shut up with her on the inside. I try to keep her off the cage top for the last hour or so of the evening, and put a sheet over the top a little before bedtime.
