You can skip restoring the Raanaar doll; it is not a required quest. The teleporter stones are removed from your inventory by design, there is just no cut scene or other explanation as to why (when the imp historian gave them to you, he said he would be back for them).
Your missing gold is a bug, as well as the crystal fragment staying in your inventory. You can 'cheat' to get the gold back;
For you cheaters out there (The Duplication Trick)Hex editing - gold, experience, stat/skill points 
