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You note that she is able to eat the hay from outside the box, so I wonder if you can arrange it so she has to go in the box to eat it. As a budget friendly option, maybe attaching cardboard to the litter box sides so she can only enter from one way to get the hay.
Litter box training can take time. My Wick is a rabbit that requires more engaged training, where I need to physically move him to the box because he isn’t tuned into the poops and pees appearing there. Some rabbits need this.
You are two weeks in, so it can take time! Plus it’s a new environment so the instinct to mark is pretty strong.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.