My wife had lung surgery in March. After surgery her ankles were swollen and one small toe felt broken (it wasn't). The surgeon, her Internest and a Podiatrist have not found an answer. Uric acid levels appear to be normal. Her feet discomfort is so bad it is grearly impeding exercise to help her lungs recooperate.
I know that this is another doctor to see, but have you tried to get a consult from a cardiologist (regarding the circulation) or an endocrinologist (hormones/glands). These are just the first thoughts that I had. I hope this helps and I hope that she will be feeling much better soon.
I had another thought. The respiratory and cardiovascular systems work closely together. Could she have suffered a low level of O2 in her system during the process, which might cause her extremities to experience some O2 deprivation? Just a thought. Talk with her thoracic surgeon. He should be able to give some answer about that question.