I just put all the finished quest items into a barrel or chest as I go along to keep my inventory clear of them.

Yeah, headvice does damage but the "blind" is broken. They still run up and hit you or the rangers target you.

The pyramid quest did close in my log so it must be an occasional bug that doesn't always happen.

On the initiation quest: maybe it is like the first time you encounter a stone; you don't need healing but it reacts to your presence anyway as it did in Cyseal.

Yes there are clues to solve the order of the buttons in the temple. Without spoiling I'll say read and look carefully while in the library.