I managed to arrest and torture Sam Riemann to admit his guilt and his accomplices. However, after this I've gotten stuck and according to Let's Plays and the forums walkthrough I am to speak with Jeremiah to start the court proceedings. Unfortunately the option does not appear to me when talking to Jeremiah, probably because I am a prosecutor myself already, and discussions with the Bishop Quentinus and Inquisitor Vallejan come up with claims that I do not have enough evidence and Vallejan simply tells me to go find more evidence against sir Edmund.

How am I to proceed? I have no idea anymore.

Unfortunately that's the problem right now! I've talked to everyone, I've tortured as many people as God lets me and nobody is spilling any new dirt on the good Judge, even though I am certain of his quilt! Any tips on what would be next logical step? It's all starting to smell like a conspiracy to me, the whole town is protecting Vallejan!

All right, let's have a closer look: You need to get a warrant for Vallarian from Prosecutor Jeremiah. Jeremiah needs three pieces of evidence against Vallarian to issue the warrant: a confession from Linda van Gallagan (saying "Baroness Linda van Gallagan confessed that she murdered the merchant...", a confession from Sam Riemann (saying "Sam Riemann pleaded that he, along with Baroness Linda van Gallagan...", and a note saying "I have found the blade of a magnificent dagger in the cemetery. Beyond a reasonable doubt, it was used to pry open the lid of a coffin from which a dead man's body was unceremoniously disinterred. Later, I discovered that the dagger belonged to Judge Vallarian." To get the last note, you need to find "Magnificent dagger blade" that can be found in Hillbrandt's cemetery (see this map: http://img853.imageshack.us/img853/1413/hillbrandcemeteryjpg.jpg) (founding it will add a note saying "I found the broken blade of a magnificent dagger in Hillbrandt's cemetery..."), and "Magnificent broken dagger" that you can obtain from Ruphert the shepherd living in the Dragon Rock location (obtaining it will add a note saying "I've acquired the hilt of a magnificent dagger from Ruphert the shepherd..."

These two confessions and these two pieces of the dagger should be enough for you to obtain the warrant you need.