I think I am going to change from the style I was initially going for. I want it to be more stylized. I think having the video footage more stylized with compliment my method of animation better then my original idea. I'm going to reshoot using more controlled lighting and the color correct in Final Cut. 

Here are some examples of styles. 

http://motionographer.com/theater/teatro-melies/

http://www.partizan.com/partizan/v.php/ace_norton_the_virgins_teen_lovers/clip.mov

http://www.qbodp.net/