So she is off the med for the thyroid, right, lol. That may make a difference in a few days.
Most of what I can suggest you would already know: moved or changed the litter box, changed the litter. Change in the house.
Do you have the space to start her in a small area (bathroom) and retrain with the box?
Changed food that resulted in the runny poop? If not, then do change it, and give something else a try?
See, you already know all that stuff!
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