Who is the father of Minato Namikaze? Does Namikaze mean a clan or is it just his second name?

I think the only way Naruto could defeat Madara Uchiha is to be in a blood-line relation with the Sage of the Six Paths, and thereby achieving a Rinnegan of his own. 

Since Kushina, Mother of Naruto is from Uzumaki clan; which is a blood-relative of the Senju clan, it will make sense if Minato is from any distant clan related to Uchiha clan.

Is there any clue revealing who might be the parents of Minato?
No, there are no clues, at least not yet (in the anime).

But your second part of question/theory is obviously incorrect, since it's not enough to be related to an Uchiha, because it's not the DNA you need (directly, as is the case with the Senju part), but rather it's the eye itself. Since Naruto doesn't have a Sharingan, even if he's related to the Senju (distantly), he wouldn't be able to awaken the Rinnegan - not even if, by some miracle, Minato were to be related to the Uchihas (it seems pretty impossible to me). So, if Naruto were to not get a Sharingan, e.g. from Sasuke, in my opinion, he will never be able to awaken the Rinnegan.

As with the fight, I've no idea about the manga; the only thing I know is that he will team up with Sasuke (from older posts, which made me crazy...), but off-topic, I think there is more in Naruto, even without a Rinnegan, which could equal AND overpower Madara.

Related to your question, we don't know anything about Minato's parents. "Namikaze" could represent his association with a clan (as in most of the cases), or it could simply be his second name.