The problem is that one camera captured footage a little higher than the other. Cropping it stretches the image, making the two aligned, but disproportionate. I tried simply putting the raw, side-by-side footage into Roxio Video Lab and it was able to make a Red/Cyan composite video. But, because of the vertical misalignment, the image does not appear 3D. Looking at the two side-by-side and crossing my eyes, I can make out the 3D image, so I know the rig works. Is there any way to fix this via video editing? Or have my hours of footage gone to waste? If there is indeed a solution, I have access to both After Effects, iMovie (though not as comprehensive), and Final Cut Pro (though keep in mind I have very little experience with this software).