Where would i find the scripts that control character creation and place the Player in the cell when you click "New Game"? I've began working on a Mod that would work best with a brand new character, however I have never changed the beginning though i know it is possible cause of http://www.tesnexus.com/downloads/file.php?id=11495.

simply put:
Where would I go in the CS to set up my own new character creation?

bump...

MQ01 controls the tutorials, and such. Have a look there first.

Take a look at the script CharacterGen (I think that's the name, it's attached to CharGenQuest IIRC). That runs the entire start sequence. A point of interest is that CharGenQuest stage 5 is where the player is moved to the start position. You can play around with this script to change things around.

One important point - some mods (particularly the DLC) will not work unless CharGenQuest has advanced to the correct stage.