First off, the stone age weapons are listed in the Ultimate Combat book where True Primitive is located and rather than saying you are proficient with stone age weapons, they give you a very specific list. RAW you are not proficient but if you bring it up with your GM, they may grant you the proficiency if there is something specific you are going for.
Secondly, as far as the trophy fetish for armor goes, the Trophy Fetish ability only specifically mentions "a suit of hide armor" for attaching your trophy fetish but then proceeds to tell you that if your armor has the fragile quality then once per day you can choose to not have it break if a crit is confirmed on you. This would imply that, Rules As Interpreted, it does work on bone armor because Hide, with a capitol H, does not have the fragile quality but bone armor does.
Finally, as far as using your trophy fetish for natural attacks, the answer is no. You can attach it to one of the True Primitive traditional weapons listed but natural attack is not on that list so you would have to ask your GM for permission in the case of like building Beast Totem, Lesser and wanting your trophy fetish attached to your hands to gain the benefit on your claw attacks.