According to the old Slaves to Darkness and Realms of Chaos the Emperor came about differently to how it is put across here. Story is in Anatolia, 8000BC. The shamans of earth numbered in their hundreds, they were immortal, every time they died they reincarnated through the warp, which at the time was a placid place and basically the natural aether. As mankind became more prominent the warp started to become turbulent (at this point Khorne, Tzeentch, and Nurgle hadn’t really risen to more than a ripple in the warp, they developed later as civilisation led to war, politics, and disease), to the point that the shamans were finding that less and less were being reincarnated and just becoming lost souls in the aether (swallowed up by the blossoming embryos of cosmic power that are to become the gods), so they gathered together to try and figure out a way to get through it.

They decided after hundreds of years of debate that they would commit mass suicide, therefore forcing all of their souls into a single entity, that entity is the Emperor of Mankind as we know him. That is the fluff roughly from those books.

As for the timing of Slaanesh, again, slightly out. It’s been in fluff that the Emperor knew slaanesh was coming and planned appropriately. Manking had spread through the galaxy in millennia past and during the Age of Strife I believe (it was one of the ages) the warp became turbulent and stopped communications between the systems, limiting the humans to intrasystem empires etc. The Emperors plan was to reunite humanity, and one of these plans was that of the primarchs, they would lead armies out from Terra to reclaim the galaxy and birth the Imperium.

So the Emperor foresaw the birth of slaanesh and the fall of the eldar and put into place the plans to unite earth under him, creating the thunderwarriors, protospacemarines. Stronger, faster, smarter than marines but genetically unstable and short lived, dying of organ failure and cancers etc. After conquering earth he set about the primarch project whilst simultaneously making improved relations with Mars, giving them pride of place beside him in return for tech and ships. He began the space marine project to have armies ready for the primarchs, who through a freak accident (some fluff suggests weak chaos gods only being able to disperse them through space and not destroy them, angry at the fact the emperor had stolen the arcane knowledge needed to create them from the gods) were flung through space.

The emperor creates the legions and waits with armies champing at the bit. Cue Slaanesh…..Booom, the psychic shockwave wipes away the turmoil in the warp that was impenetrable to space travel leaving the route for reconquest open. Out shot the expedition fleets, lead by the emperor, reclaiming human colonies into the Imperial fold, either by force, peace, or destroying them outright if they were uncooperative. the difficulty in the warp was the turmoil caused by slaanesh awaiting birth, the birth actually cleared it.

That puts an interesting spin on the eldar, as it means their vast galactic empire only died the moment the emperor left on his reconquest.

As for what he did in his time, yup, he had babies, the star child thing is accurate, they were called the Sensei. They were immortal beings, in the early fluff they had the ability to project essentially Antiwarp beams that would cleanse warp taint in whatever it touched, later this seems to have been retconned to the fact they are all pariahs and lacked any kind of presence in the warp. The old background actually states 8000 B.C, so it is fair to assume that it is in our timeline, backed up by the fact that is stated he was wandering for millenia, always the power behind the throne, guiding humanity to where he needed it to be, I believe it even mentions he was a force behind the Roman Empire and the (given that it was written by brits, a bit self aggrandising) British Empire. I believe those two were mentioned in actual fluff by name.