The short blunt answer: you gave her too much freedom too early and you no longer have a housetrained dog as a result.
But you can fix that.
Most puppies are not really reliable or able to be trusted to have free rein without supervision across a house until around one. The first signal that things were going awry was her ignoring the toileting space -- from her perspective, no one was reinforcing this as the positive, rewarding option so why bother going in just one spot when any spot would do? This then transferred to the house, because if no one reinforced her outdoor choice, and she could run wherever she wanted through the house without supervision, why not go indoors?
While to us humans the difference between in and out is quite clear, to a dog it isn't at all. It's just another space in which to go, and because a dog is housetrained at say 3-4 months not to go in the kitchen, this isn;t transferrable knowledge to the rest of the house. Another room to a dog is no different from the 'other room' of going on the lawn, the dirt, etc.
You need to only give a dog access to room by room as it becomes absolutely reliable in each room. But even then, really a dog needs to be watched constantly until around 9 months or so as they are too young to hold firmly the idea that this area here is OK for weeing/that over there is not. It is like expecting a toddler to be fully toilet trained after two weeks of using a portable potty. Puppies are still just babies to children at these ages and much that is remembered for a day or two is forgotten the thrid day. It has to be constatly, positively reinforced through praise and treats while at the same time, the dog must NEVER be given the opportunity to stray from the desired behaviour. That means watching her like a hawk *at all times*.
Positive reinforcement and reward hand in hand with total supervision are the combination that get a dog housetrained.
If you don't have it I suggest buying Shirlee Kalstone's book on housetraining a dog in 7 days. Meanwhile you'll need to start back at square one with housetraining as she needs to relearn what is OK and what is is not from the very start. Close off all those other rooms after spot cleaning with an enzymatic cleaner, get her back on the lead for trips outside, make sure trips a to relieve herself are structured at regular intervals, always have her totlly under control -- in a crate, on a lead, or at arm's reach when she is awake. Don't let her just use the doggie door to go and assume she has gone. You need to verify she has gone so you know when she has relieved herself and can be considered safe' inside for a stretch of time before the next trip out.
The good news is, that as she is already somewhat housetrained this will go faster than when she was first learning
but you will need to approach it as if she isn't housetrained at all -- as effectively, she IS no longer housetrained. Frustrating I know but we have all been there to some adegree, at some point, with some dog!