Scott_Clean: So, I arrested the heretical conspirators behind the kidnappings and burned them. I also got the necromancer soldier and burned him too. I took the test, and became an Inquisitorial Judge.
Now, I got Tinthan to steal me the Cardinal's documents, which I figure would be incriminating proof to place him under arrest. But I have no such dialogue option when talking to him or Welfar.
What am I missing?
You need three pieces of evidence against Cardinal Truncquillius since he is a prelate.
The first evidence is the confession from the third conspirator behind the kidnapping.
The second evidence are the incriminating letters Tinthan stole for you.
The third evidence is the witness testimony from the head of the Glatzburg chapter of the Brotherhood of the Righteous Master Dieter von Gelbendiel that he witnessed the Cardinal preparing the heretical mass. He should approach and speak to you about his offer of exchanging that information for information about the missing girls in Glatzburg when you approach their chapter in West Glatzburg. (As a priest and have maintained good relations with the Brotherhood of the Righteous, not certain if he will respond or say things differently on other characters or if you arrested and tortured his fellow brother in Hillbrandt earlier.)
To complete this task, you need to speak to the person at the square (near your arrival site) in West Glatzburg Guss Halworth and agree to recover his gold seal ring that was stolen by the bandits for him. Go to the Wasteland and you should be attacked by a bandit upon arrival. Defeating the bandit will drop the ring. Return it to him and he will tell you he witnessed the merchant Alphonso DiCerbio carrying out the kidnapping of Tom Clifford.
Confront Alphonso at the market square in East Glatzburg about this and he will give himself away. You can arrest him or accept his plea bargain. The former will result in a fight and subsequent surrender and all the items he was selling will be added to your inventory for free or drop to the ground as forfeiture of property, but soldiers may attack you and cause you to lose alignment. Arresting him and then interrogating him without torture or accepting his plea bargain in either case, he will point to Duke Rowan van Leerin and the Devil's Caverns.
Travel and fight your way down to the third level of the Devil's Caverns, defeat the lizardman chief, take its key to reach Tom Clifford and offer to bring him home. Return him to Johannes Clifford in Duke Rowan van Leerin's house and Johannes Clifford will tell about the duke's part in the kidnappings and the secret basement beneath the house and give you the key. Enter the basement, confront Duke Rowan van Leerin, defeat him and take his journal. Return to Master Dieter von Gelbendiel and present to him the journal, the confession from the duke and the witness testimonies from Alphonso DiCerbio and Johannes Clifford. He will give you the witness testimony against the Cardinal in exchange.