She sounds quite stressed. The first couple of weeks is settling in time in their cage so if you've cleaned it out or changed anything that will really stress her. I'd suggest going back to square one if that's the case. Leave her alone for 2 or 3 days in the cage (unless she shows signs of wanting to come out). And let her settle building her nest and deciding where to hoard and pee etc. And don't clean or change anything for two weeks. When you know where she is peeing (often a corner of the cage) you could take a handful of the wet substrate out -but i'd leave it over a week before doing that. Add a handful of new substrate and mix it in and then pop a litter tray in that corner. (Linked below). That way the cage will stay clean a long time. They need at least 3 to 4" deep of substrate so if there's less, add more now before giving her the settling in time for a couple of days. They also need somewhere dark to retreat to in the cage - a good sized house eg. If there isn't anything like that, pop a shoebox or tissue box with a hole cut out in there (she'll probably make anest in it). If you have a bendy bridge, you could put it over the house door so it's darker inside.
Also does she have a wheel that's big enough? Their cage is their territory and their environment so if they don't feel safe or settled in it (ie if they feel invaded) they try and escape and are desperate to get away. So avoid the temptation to tinker with it or change things or move things round - except for the initial changes before leaving her for a couple of days.
The water bottle hole is a very common place to get chewed - sticking a screw in toy in that hole tends to prevent it (see link) - you can attach the water bottle inside with velcro instead or use or make a bottle stand.
Put lots of torn up strips of plain white toilet paper in a big heap somewhere in the cage (but not inside the house - they like to forage for it). Scatter some food and hide the odd treat when you've got it just right so it'll distract her.
Don't clean the cage out for at least two weeks now. They don't need weekly cleans if they have enough substrate and a litter tray it can go a couple of months with just the occasional spot clean - you just empty the litter tray every five days or so.
https://www.amazon.co.uk/Hamster-cor...=hamster+potty
https://www.amazon.co.uk/Supreme-Pet...hinchilla+sand
https://www.amazon.co.uk/Ancol-Woode...ds=carrot+chew
https://www.amazon.co.uk/Superpet-Ka...HHZEAHTY2F0HVR
The chinchilla bathing sand goes in the potty
Also added a screw in ledge rather than the carrot chew - something to sit under - might be better and also blocks the hole.
It also sounds like she isn't hand tame yet so not easily handleable. After leaving her to settle then doing some bath tub taming is probably the next thing (dry bath tub with the plug in and a couple of toys (eg a mug on its side, a tube) she can't escape from there and you can gradually get her used to your presence and slowly used to being stroked/handled - post about that some more when you're ready!
So right now it's time and patience.