I created a command line tool that executes a lua script. Functions are exposed to lua for the purpose of loading and manipulating images and creating movies frame by frame. I call it MovieFrames. I used the CxImage image classes for image processing. This automatically gives it a lot of power to play with images.
So now I just need to write a lua script to process the artwork and bam I'm done. No more manual cropping, cut and paste, frame-by-frame nightmare for me.