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Just to not spoil too much with the topic...

...I'm looking for Cardinal Truncquilius after telling Welfhar that I'm planning to persecute him.
He just... ran off. While Valarian turned up at a fairly obvious spot, I can't seem to find where Truncquilius went.

I'd like to add that my King Harlior quest is bugged, my Istwan de Bragho quest is bugged and I whatever quest is connected to the undead in the sewers may also be bugged.
On top of that I'm not sure if Father Frederick is an actual person I can find or if his diary is all that's left of him.

Just in case any of that matter.

Thank you for any advice you may offer me.
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cardinal is in the cathedrals dungeon. i'm sure all other quests are not bugged also. i played the game till end and didn't find a single bug.
Thank you once more for your reply. I've suspected as much.

However this does raise another obvious question: What do I need to do in order to enter them?
I'm specifically referring to the door leading south east into said dungeon as I have not found myself able to open them using either brute force or levers of any kind.

Regarding the other quests that I consider to be bugged: I've read several threads on the forum indicating that depending on actions taken by the player possibly not intended by the developers those quests may get stuck. Especially the Istwan one.
I have no doubts that you may have been able to complete the entire game without encountering the problems I'm experiencing but chances are that I have just... screwed things up.

Either way, I'd really appreciate if someone could tell me what the requirements are to enter the tunnels beneath the cathedral. I've kept all quest items I've found so far so I'm confident that I might have just missed something as opposed to having navigated myself into a no-win-scenario.
Your best best is to wrap up other loose ends. Make sure you've arrested, tortured and executed any heretics. The game will work itself out if you actually play it, rather than worrying about where somebody went.

You're not necessarily supposed to know where someone went. That's part of the mystery. So again, play the game and all will be revealed in its proper course.
Once Truncquilius runs off a monk will spawn next to the door who you can talk to, it's very easy to miss.

There are definitely bugs in the game but the ones you mentioned may not be. For the sewers you have to pixel hunt carefully, pulling all the levers will open the gates, you may have to do it twice. If you didn't pay attention to the banter, father Frederick was priest that retired in Glatzburg, he died years ago. And how are you stuck with Istwan? He is supposed to be immortal the first time you encounter him.
Can you enter the dungeons without killing the monk gatekeeper and everymonk around ?
The guy says I can't order him around and won't let me pass.
No, you can't enter the dungeons without killing the monk.