At the OP, at this point in the manga, it is not likely we will be told many more secrets. Kishi has touched on everything you mentioned, several times in some cases, so they are not likely going to be touched on again considering we have now been told the ultimate secret of the manga; the original origins of the sage (sage's mother) and Juubi.
Madara was never watching Obito. He was, however, watching Nagato. Obito happened to stumble into his lair, it was literally a chance thing Madara obviously did not plan it. Once this chance thing occurred, Madara pounced all over it and took advantage of the situation, but you better believe that Madara did not plan on meeting Obito in the first place.
Madara likely stole that single sharingan on his way to give his Rinnegan to Nagato. Perhaps he killed a group of Konoha shinobi along the way, and could only collect 1 sharingan from a dead uchiha before having to move on. Perhaps he damaged one of the eyes while killing them or perhaps reinforcements were on their way and he only had time to extract one of the 2 eyes, I don't know. But it seems obvious that he collected that eye prior to giving his eyes to Nagato.
As for Obito returning to Madara, Madara was simply overconfident. He was thoroughly convinced that Obito would loose his trust in the world and wish to follow him. Now
it IS possible that Madara orchestrated what Obito experienced in regard to Rin's death, or made a genjutsu out of it, but all of this would have been planned after meeting Obito. Again, Madara never planned to meet Obito in the first place, he simply adjusted his plans once he did.
I think we have seen everything relevant to the Uzumaki clan origins that we will ever see.
I don't think we will ever find out exactly how Hashirama died.
I think there is still a chance we will be told about Nagato's origins, but only if his origins lie with Madara (perhaps his grandson).
My take on that is the age of the DNA used.
Kabuto said that he "Grave-robbed" to get the DNA needed for the jutsu. So, this DNA is litterally taken off the dead body.
But, in Madara's case, he didnt know where Madara's grave was, so he looked for some at VOTE. Once he found some (surprisingly), he could resurect Madara from the time he was at VOTE. He also implanted some of Hashirama's cells (which Oro has cultivated, and used in his experiments) into Madara's stomach. Since Madara had EMS, and Hashi cells, he obtained Rinnegan again.
OT good post
I think the manga has strongly implied that Madara's DNA was taken from when he was old. Now I think its possible for DNA taken from when he was younger to revive him in a younger state, but I simply believe that the manga has implied differently.
Thing is, Kabuto
did not know whether or not Madara had Rinnegan. If he caused Edo Madara to re-awaken Rinnegan, he likely would have seen the transformation. In addition, Kabuto made it clear that he brought Madara to a state beyond his prime and made his edo tensei special. This strongly implies to me that Madara was brought back old and Kabuto simply manipulated his body by adding Senju DNA.
Lastly, the fact that Madara had full use of his Sharingan/ EMS/ Rinnegan strongly implies that it was unaltered. Therefore, I strongly believe that he was brought back old and manipulated to be younger because his old body at one point had access to all three of those Jutsu at once. Yes Madara died without his Rinnegan, but he at one point had full access to all levels of the doujutsu and therefore Edo tensei inherently grants him access to the greatest form of his Doujutsu while alive.