So archaeological evidence shows that after the Trojan war Troy was re built several times. So what was the state of Troy during the Greek golden age when Athens and their allies were fighting off the Persians?

You might find something interesting in this thread from a month ago -- my first post there mentions one incident relating to Troy during the Persian Wars, in fact. Herodotos 7.42-44 is the relevant primary source. I don't want to repeat myself, but do feel free to ask follow-up questions.