I was in pretty close to the same place and stuck because I didn't realize there were four wide doors instead of two in the main hall,
(Thanks to tapewolf for the hint that helped me along.)
A few suggestions:
* I assume you need a key to open the prison. By continual searching I did ultimately find the prison key (as well as a readable telling you what you need to find in the prison). The lock is almost invisible on the left side of the door.
* Search the library for readables. You'll need 'em.
* Once you get as many readables as possible, you'll eventually need to solve the puzzles
There are readables telling you what you need to do here and giving hints for
I was able to solve it on my own in one evening although I didn't believe it at first, given that I had all necessary readables. This will give you a key you need to move the plot forward. (Once you solve it, enjoy the happy music... you're basically done with puzzles, you're just going to be avoiding undead - some really scary - for the rest of the main mission.)
By the way, this was a very impressive mission!