Ha ha - she is telling you to keep your hands out - maybe why she's biting. No they don't like people ruffling up the bedding etc - they like to do that themselves
It's necessary sometimes f you need to do a spot clean but rarely rather than often.
I think there may be something to do with access as well. An easy route onto a shelf tends to make them feel more secure. Its maybe just not quite how she wants it - along with the changes. I find the rainbow bridge can be a bit unstable as well when it's on the substrate.
You know one thing I would do - without waiting two weeks - is take the long bendy bridge out and put a house there instead. if that is the corner where she is nesting and chewing - it will distract her from chewing in that corner and keep her busy settigng up home in the house.
Hamsters aren't that good at climbing and don't see well -so they do it but arent that happy about balancing. Charlie - nervy thing - was terrified of stepping onto anything smaller than an 8" square thing!
As she's so stressed at the moment then I think one more change - ie adding a shoe box house now and eithe removing or slightly raising the long bendy bridge so it can still be sat under - may actually help her settle a bit.
Then leave any other changes till another time. Does she actually need to get to the top shelf? ie for food or water? Or is it just somewhere to go. Because if she needs to get up there and finds it not quite as simple as running up a ramp then that could add to stress.
I think longer term I'd just have the one shelf at that end and have it easily accessible lower down direct from the substrate - you can always hang something over it for interest.
But for now I'd just add a house at that end. Do you have a normal bendy stick bridge thing that turns into a tunnel? If not doesn't matter. If you do then you could put that over the shoe box house entrance. Seeing your cage i think a shoebox house would fit well at that end and be as good as the Ferplast one and maybe even slightly bigger inside.
Things like chews - I just leave them usually for a while. If I take an old one out I put a new one in. Our current syrian likes to keep chewing at them even when there's no food left on. They also tend to chuck anything out of the house themselves if they decide it needs removing sometimes. ie if you've left it a bit long.