It might be easier to make a good mod with this in mind and simply make an 'Alliance' and 'Horde' faction without all the trouble.I think the eras should be:
The First War (first invasion of the Horde through the Dark Portal)
The Second War (when the Elves, Dwarves and Gnomes team up with the Humans and the Trolls, Ogres and Goblins team up with the Orcs)
The Third War (coming of the Burning Legion and the Undead Scourge)
The Present (World of Warcraft-time)
King Terenas II, Supreme Commander Anduin Lothar and King Varian Wrynn for leaders of the Alliance.
Warchief Blackhand, Warchief Orgrim Doomhammer and Warchief Thrall for the Horde.
But let's see.