I don't know much about the Marvel universe, so I am basing the following on the information given in your question.
Physically super-superior in every way
seems not too unlikely. If you compare an average human to a top athlete like Ashton Eaton, the differences are striking. Hence, I would argue that most of what is needed to become "harder, better, faster, stronger" is already embedded in the human genetic code.
How do you get all humans to become more like that? Well, only those people mostly resembling Thors anatomy are allowed to reproduce: Forced selection of partners based on individual genetics will help to evolve super humans over time.
live about 5000 years longer than us
This seems to me the more difficult part. Negligibly senescent humans are a dream of distant future. However, you might want to read up on the wikipedia article about research strategies to neglect age-related damage to human tissue. From the article, you see that DNA mutations, junk protein, cell loss, loss of cell division capability and changes in cell linking protein all contribute to ageing in humans. Cancer and degenerative diseases are common consequences.
Summary: In my opinion, the human anatomy is already quite close to that of Thor and the way to get there is theoretically known. However, to reach the desired age, several profound advances in different fields of medicine and biotechnology that are currently far from reality, have to be achieved.