While you may have deleted it all (it is for the EGR and smog pump systems), the computer does not know that. You will either need a chip for your computer to turn off all that stuff, or some way of faking the signals so the computer still thinks the parts are still installed and working.
I recommend the chip. Moates.net has a reasonably-priced chip-burning setup you can buy for a little over $200, and you can start doing your own tuning as well.