Penumbra overall storyline and a few questions?

[Yuhaney]

Who exactly was Red?

Red was one of the mine workers. His real name is Tom Redwood.

the whole requiem was in his mind and made up?

In mind, yes.
But not made up.

and he woke up at the end of overture or was it the end of black plague?

No, it was the end of Black Plague (same room you sent the email from).
As you see, when Requiem starts, you get knocked out by one of the Infected because you betrayed the Hive mind like Clarence did.

and If it was at the end of black plague then how did he get all the way back to the beginning of the complex near the incinerator?

He didn't get back to the incinerator.
That was in his mind while he was unconscious / dead.
You decide this in the end of the Requiem, you can either join in with Red to die, or leave the room and start the whole story from the beginning, which means (if you look from the part of the Hive mind) a new possibility to do the right thing - destroy all the evidence.

I understand the artifact's in the first two games were tuuringait things helping to spread the virus, but what I don't understand is in requiem there is some other kind of artifact (i think) and you need to have them all to get the good ending of requiem.(supposedly)

No. Nothing like that.
Those are just so you can get the password in the end of the game.

Who was the shadowy figure at the end of Penumbra Overture?

There is no known answer for this question.
But I believe it was one of the Infected to attract you to a trap.

Also how come they took you prisoner if later in the game overtime they see you they want to kill you? And at the end they don't want to kill you?

You were already infected with the virus, so you were part of the Hive mind and Hive mind works together (as said in the end part of the Black Plague).

Clarence showed up later, and in the end, Clarence had selfish goals that made them attack you to kill Clarence.
But since you remove the virus (Clarence) from your body, you were not the primary target anymore - Clarence was - and they killed him.

Why they didn't kill you after that?
Hive mind had plans for you, same plans it suggested to Phillips father.
And those plans were to destroy any evidence leading to the mine so that the Hive mind would rest in peace.

But the email you sent, told exact coordinates to the mine and told Phillip's friend to get there and kill the Hive mind.