Ordered the American I.P.A. kit and I thought everything was going great until I noticed a bag of Pilsner extract sitting on the counter top after the beer has already been placed in the fermentor. Any ideas on what this will do the final outcome of the beer?

Well, it will definitely be lacking in the alcohol department. This will also throw the balance of hoppiness. You could dissolve the extract into the wort and then pitch the yeast and you should turn out fine. Maybe a little heavy on the bitterness, but hey, it's an IPA.