Using command blocks I generated villagers that sell custom items (for example, "paper" with a name, lore, and a damage value of 10)... using a damage value allowed the game to distinguish this was not regular paper and that it shouldn't be used for crafting, and the NPCs were able to identify it and only trade for it specifically, and not for regular paper. This was the only way I found to prevent improper trading.

Now the textures on these items are missing (and has been since 14w26a), and I believe it's the damage values that's causing it.