TwistedFocus - Thanks for your help man!
I ended up having SCT send me a stock tune file for my car, it is completely neccessary to have even when loading a custom tune on top of it. When the software, company and your gut tell you to back up the stock tune, DO IT!!!
I would like to thank SCTflash, Jon Lund Racing and CR member BIGHairDryer for your help.