Fatty liver in its early stages might (not necessarily) mean obesity but, in its final stages means a bird that is terribly skinny because the body can no longer utilize properly the food it's ingesting (if the filter is clogged, nothing goes through) and cannot get rid of the toxins (again, the clogged filter) so, literally, the death is caused by both poisoning (the reason why she couldn't keep her balance, her neurological system was shot by the toxins) and starvation. One of the signs of birds with severe liver malfunction that the end will be forthcoming is an insatiable hunger combined with lethargy; the bird swoops down on its food and eats and eats like there is no tomorrow and, immediately after, goes to sleep (a bird that goes to sleep immediately after breakfast is not a 'well' bird) but, when you check him out, you see that the bird is not only not gaining weight, it's actually losing it (which makes no sense if the bird is not moving and eating and eating, right?). Yes, Carla died of hepatic lipidosis (the enlarged liver and her low weight are a dead giveaway, if the vet had done a necropsy, he would have found a liver that is not only enlarged (the body tries to compensate for the decreased function by enlarging the organ) but also discolored and falling apart and, when opened up, riddled with fatty nodules), no doubt about it. And, I don't mean to be harsh or scare the bejesus out of you but Jelly Bean will too if you continue feeding her animal protein (herbivores cannot digest it properly, they lack the necessary enzymes because nature never meant for them to consume it) and free-feeding vegetarian sources of high protein. With a possible couple exceptions, no parrot species was created by nature to consume animal protein. Period. (Have you ever seen a NatGeo documentary of parrots hunting other animals?). And amazons are more prone to fatty liver than other species because their natural diet doesn't contain that much protein. Human food is simply not good for them because, plainly said, supermarket food is crap... too many simple carbs, too processed, too refined, too much salt, too much sugar, too much fat, too many preservatives, everything GMO, etc. You need to put her on gloop or a similar dish with organic raw produce for breakfast and all day picking plus a small, measured portion of a good quality lower protein seed mix (a safflower-based cockatiel one, for example) for dinner. You can continue using roasted, human grade tree nuts as treats but not a lot on a daily basis (like two almonds, hazelnuts or pistachios but one whole walnut, pecan or brazil nut).
Now, getting her up at sunrise is fine but she can't have any artificial lights on until the sun is out and the sky is completely lit (you didn't say if she got up to a full lit room, I am assuming this is the case because this is what humans do) - and covering her cage after it's dark doesn't do it, either. She needs to be exposed to the sunset without any artificial lights and, once she falls asleep with nightfall, then and only then you cover her cage. The trick is for them to be exposed to the change in spectrum during twilight and to wake up and go to sleep gradually and naturally. This is what sets their internal clock.
Now, as to her screams... no, she is not a baby. At almost 3 1/2 years of age, she is a full grown adult and I suspect already too hormonal which might be part of the cause for her screams. Of the eleven I've had under my care, only one single amazon was a screamer and she stopped in a matter of a couple of weeks once she was here (she also plucked her chest and was MEAN MEAN MEAN

). She could also be 'fixated' on you (regard you as her mate) so pay attention to exactly what you do when 'cuddling' in the evening (which, by the way, it's the wrong time of the day for it) because there might be some improper touching (do you caress her back, cup her body with your hand or allow her to burrow into your lap, clothes, sofa pillows?).