Thanks for the reply Lacero. I ended up doing something similar to what you suggested, only I used the garbage matte instead of the motion tab. The trick that I was missing was to duplicate the clip on the next track up and composite the color corrected/garbage matted clip with the original clip.
Espnetboy3,
In this case, the Photoshop method wouldn't have been practical because the clip is too long. The way I figured out to get the effect to only apply to the matted area is to apply both the effect and the garbage matte filter to the clip in question. Make sure the garbage matte is on top in the filters list. The effect will apply to the whole frame, and then the garbage matte will cut what you don't want out. You then composite this (by placing in the next video track up) with the original clip. The end result is that the garbage matted filtered portion of the video is overlayed on the unchanged frame, and you end up with the exact same result as you would get by only applying the effect to the specific portion of the frame selected by the garbage matte.