Since Stone and Bronze Age societies were primarily on the barter system, the assumption that everything is based on a currency value will cause you problems the moment someone wants to make a magic item. I recommend that you sit down and decide right now what arbitrary costs the "GP value" of items will represent in your world. The real costs of items depends on the time it takes to do all the jobs involved in making them, the skill required to make them, and the raw materials - which also represent the time and skill of gathering them - that go into them, including personal magical power. The weaknesses of the currency-based d20 magic item creation system will leap out at you in the context of a barter system and be much less easy to handwave than they are in the default setting.
Personally (since I've researched the late Pleistocene extensively), I found "From Stone to Steel" disappointing, as it does a poor job of explaining and simulating the reasons for a shift from a stone to a metal economy. "Primitive" tools do not do less damage than their metal counterparts. Bronze was superior to stone in that it broke less easily and could be fashioned into larger, more varied shapes; inferior in that it had to be made by specialists and was expensive to produce (tin being hard to come by and the process of working the metal being a long one). Anyone who used a stone tool could make a stone tool, and rapidly, too! The shift from stone, bone, and wood to bronze was part of an overall shift, mediated by agriculture, from generalist lifestyles to specialist ones. The shift from bronze to iron and steel occurred because iron was cheaper than bronze, requiring only one kind of easily-acquired ore once the process of extracting the metal from the ochre was understood. Iron tools were inferior to bronze ones because iron was softer. Once tempered steel was invented, iron became the preferred medium for weapons.
I don't know how big you and your group are on game mechanics and rules tinkering, so I won't make specific suggestions beyond sitting down with the people in your group who enjoy house rules the most and thrashing out a system that is acceptable to everybody. A group of heavy simulationists will want a more complex set of rules than a bunch of munchkins, who will want you to handwave a lot of stuff; a group of tinkerers can have a field day; a group of heavy roleplayers will want simple rules and be inspired by the challenges of playing a Stone Age generalist encountering a Bronze Age specialist culture for the first time; and so on.
If I ever run the vague Stone and Bronze Age scenarios I've been carrying in my head, I will not be using d20, as the assumptions behind the rule set are not compatible with the level of simulation that would make them worthwhile. I have not found another system that would do the trick, as point-based systems like GURPS and Heroes rapidly become clunky. If you can put together something fun for your players which is different enough to reward the effort, more power to you and I hope you post some details of how you do it.
