Story things I need clarified *SPOILERS*

[Bad doggie. DOWN.]

I just finished the Penumbra series, and it is probably the 2nd best single-player video game series I've ever played, right behind Half-Life/Portal. Of course, a lot of things didn't make sense, like the ending of BP and pretty much everything about Requiem. So here's some things that didn't make sense for me:

*OBVIOUS SPOILERS AHEAD*

1. Why are the animals so large and hostile? (This probably got explained in some note in Overture that I either missed or skimmed over.) Did the Tuurngait virus cause this?
2. What exactly is Red's story? He was trapped in the mine at 14, and that's all I know for sure. He was infected, right? When exactly did he get infected? Was he still in the middle of transforming when he died, like Phillips was when he got Clarence into his head, and that's why he wasn't allowed to kill himself?
3. What's up with Clarence? Why did Phillip have such an abnormal reaction to the virus? And why was he trying to get Phillips killed if he was so concerned about staying alive, as shown by when you're about to purge him from you body. Also, when he's messing with your memories, he says he's going to erase the memories of Red, but in Requiem those memories are clearly intact.
4. What's up with Dr. What's-his-face, the one who tries to saw his hand off for you? You hear him sawing something off, then a red piece of meat flies (not his hand) through the window and he attacks you, with his hand intact, I think. And why is he in Requiem at all, what's his purpose there?
5. What's with the bullet holes in the one window in Black Plague? In BP, about half way through the game, there's a window, that if you examine, says that it has bullet holes, and says that Phillips hadn't seen any bullet holes before.
6. Why is the Tuurngait seemingly omniscent? He only controls a small colony of zombies, I don't think that makes you the automatic master of the universe.
7. Why did Howard kill himself? I think this relates to the Tuurngait's omniscents, and some cop-out about it being too much knowledge for Howard to handle.
8. Why does Phillips try to get the Tuurngait killed at the end of BP? Is it out of fear, for free will, revenge, or what? And what does that have to do with him empathizing with Clarence? And why does he empathize with Clarence in the first place?
9. Why does Phillips say in the email that it will be good if he dies, and "we will all perish" if he doesn't?
9. What exactly happens in Requiem? I know that most of it takes place in Phillip's dreams after he is attacked by a Tuurngait. But why is he attacked by a Tuurngait in the first place? Does the hive mind read his thoughts while he's typing the email and decide to kill him for his betrayal of trust? And if it's a dream, why does he keep reading the diary of a man that says he's been here before? And what's with the ending where you don't get incinerated? And if you do choose to be incinerated, in that last scene is Phillip supposed to be dead in real life, too?

I'm probably gonna play through the series again soon, and I'll probably think of more questions soon. I just wish the devs would come out and clarify some of the plot points in the game.