I'm not a native Greek speaker, but I do know the answers to your questions. 1. Με πονάει το στομάχι μου. => My stomach hurts ME. "Με" is the direct object (accusative case) of the verb "πονάει". 2. Word order in Greek can be flexible. Putting "με πονάει" first emphasizes the fact that this person's stomach hurts. The subject (nominative case) of the sentence is "το στομάχι".

There are 2 ways to express that you feel pain somewhere in your body. You could say " πονάω στο στομάχι/ πόδι/ χέρι μου" which means "Ifeel pain in my stomach/ foot/ hand" or you could say" με πονάει το στομαχι/ποδι/χέρι μου" which means" my stomach hurts me." the first one means that I am hurting and the second one means that my stomach is hurting me. The sentence has a different subject and different structure as well but they both mean the same thing. The "με" in the second sentence is the object.