Reading some other threads about the Emperor, it struck me that the Emperor may in fact be a kind of Warp Daemon. In Realm of Chaos it is stated that independent daemons are sometimes generated by mortals. What is needed is a commonality of experience and geographic proximity. Events such as traumatic disasters or a heroic last stand can cause the shadow selves of those involved to flow together and create an independent daemon. There are actually death cults whose members live as murderers to establish a commonality of experience. They will then come together and commit suicide in the hopes their souls will merge in the warp and create a daemon.
Was this process used to create the Emperor? The Shamans would have shared a commonality of experience. When they killed themselves at once in the same place, their geographic and temporal proximity would allow their souls to merge, creating a new daemon that embodied the hopes of the Shamans to save humanity from Chaos. What would be needed next is a way to incarnate the daemon in the Materium. To do this they would choose the greatest of their numbers, and a few remaining Shamans would actually perform a ritual of possession in him (or perhaps he performed to ritual on himself). Through the ritual, the Daemon would enter its vessel, merge with it and become the Emperor.