Had an appendectomy two weeks ago. just started to have lower right abdominal pain along with nausea and low appetite.

Call your doctor: This is something that should be seen by a doctor in person, as you will need a proper physical exam. Please call your surgeon as soon as possible so he can see you. If you develop a fever or the pain gets worse, you should go get evaluated in the ER.

See a doctor: Your pain could be related to the PCOS, or menstrual cycle pain, or adhesion formation after surgery. However, 2 weeks after surgery another possibility is an abscess formation. Typically they form 7-10 days after surgery. It's not uncommon, and needs to be treated promptly. See your surgeon to make sure nothing further needs to be done.