Stone age, eh? I'd love to hear more details -- I've been thinking about running a stone age 4e game myself.
Not much to tell, yet.
I'm basically running the Book of Genesis, starting with the PCs trying to stop the god of desert storms, El the Eternal, from flooding the world in an effort to destroy the worshipers of all the other gods. It's raining, and if they don't stop El within 40 days, all their people will be drowned.
Each of thirty different villages sent a 'champion' and a few lesser warriors to aid the mission, and now they are marching from the first proto-city in the world, Eshkital (loosely inspired by Jericho), across hostile terrain, to the desert where they will face El's followers. Their current plan is to find the 'great wooden ship' the followers of El are building, then storm it so they can hold El's followers hostage in exchange for stopping the Deluge.
Roleplaying wise the game has been great, because each player got to make up his own primitive tribe, and what god his people worship, and design their own style. Everyone has their own special contribution -- the fire shaman's flames can withstand the rainfall, the warlord comes from a village with lots of giant insects whose chitin provides the only quality armor, the monotheistic warlock has unknowingly befriended the angel who is spying on the expedition, and the warrior fisherman worships He Who Writhes, a giant kraken who will come in handy when its time for the PCs to assault the Ellish ark.
Game rules wise, I really haven't changed anything. I just made metal unavailable, which shifted some character design choices a bit. And since I didn't have a full sense of how to make NPCs, and there are a LOT of NPCs (I'm sort of inspired by Lost in how I'm interweaving backgrounds), I just made each NPC have the stats of a monster that I felt was thematically appropriate.
Everyone's human, but the leader of the whole expedition has stats of a hobgoblin warlord/captain/something like that; and the shaman who loves swarms has the stats of a stirge.