What Have I Missed!

[Metathron]

I think the problem might just be semantics for some of those things, since if you've finished the game, you can't have missed the gremlin boss, Zilgadis, who possesses one of the stones.

An ancient knowledge scroll gives you 50% more experience for the next 5 battles. They are rare and precious, so naturally reserved only for those battles that yield the most experience, i.e. bosses & strong heroes.

The spider is in a cave on Dersu Island.