Okay, time to get the knuckles cracking.
Why are there no female Mogu? Good question. Vykrul, Dwarves and Gnomes all had them, so why should Mogu be an exception?
Easy, they aren't. There were at one time Mogu females, Monara is proof of this. Look at the Twin Consorts dungeon journal again,
The Twin Consorts are said to be greatest of the Thunder King's treasures. Rumored to be the only known female mogu in existence, Lei Shen keeps his trophies close and their combined arsenal against interlopers closer.
Rumoured. Remember, the ones keeping history on everything Mogu are Pandaren, who had there history and scrolls destroyed when Lei Shen rose to power. Any records of female Mogu before Lei Shens rise would be lost. Mogu females at one time most likely existed. Why did Lei Shen kill them? Simple, men are better at fighting, after he took Ra-Dens power and reversed the Curse of Flesh, he realized they didn't need females any more. They would be useless, and also, they run the risk of birthing another 'Lei Shen'-type Mogu. He would much rather just have mindless, soulless constructs in his empire than run the risk of someone coming along who would want to over throw him.
This brings me to Mogu age. I do think Mogu are actually immortal, which would explain Shan Kien and Iron Qon. But if they are immortal, how did Lei Shen die of old age? Well, thats when we have to start speculating. My personal belief is that Lei Shen is so absurdly powerful that his body can't sustain it. It is says he charges like a battery, so maybe, he looked around, was happy with the empire he made, and simply let himself run out of power. It would explain why he is so ashamed of the Mogu when he is ressurrected.
And about Mogu history, remember, pretty much every archaeology find in Pandaria was written by the Pandaren. One of two things most likely occured:
1) They didn't know the full story of the Mogu and Saurok, so they just assumed how they came to be.
2) They don't want people knowing that Mogu are born from the Titans, as it may change their perception on them.
Personally, I see 1) as bring more likely, as like what was brought up in this thread, history isn't always right.
Now to the fun stuff, Ra-Den. There is no set in stone theory, pretty much everything is unknown, all we have is theories, and here is mine.
After the Titans left, all the Titan Watchers and Keepers, aside from Tyr, fell silent. The Titans left thinking everything with the Old Gods was good, but they were horribly wrong. So the Watchers isolated themselves from the mortal races, as they looked at ways to contain the Old Gods (Galakrond, we will find out, was one possible solution Tyr thought of). Ra-Den was dealing with something else though, the Sha. He was looking for a way to contain the Sha, and Lei Shen came up to him with a proposal; Give him the powers of the Titan, and he will create a strict empire that will follow society the way the Titans intend.
Ra-Den was intrigued by this, so he gave Lei Shen a portion of his power to do so. And Lei Shen showed his loyalty be immediately ripping out Ra-Dens heart and keeping him prisoner. He tortured and experimented on him, which led to things like Anima and the Divine Bell. This is why Ra-Den is so depressed and angry when we fight him. The last time he trusted mortals to do the right thing, he was mutilated and kept prisoner for 15k years. Actually, maybe the other keepers heard of what happened to Ra-Den, and this is why they fell silent? Who knows.