Quick Update
Now that I have a transcoding system, I have started looking into how to manipulate the motion vectors of certain frames - at the moment, this hasn't yielded any progress. Whilst researching this, I am looking into developing an AES cryptosystem for encrypting the embedded data.
I have also started trying to get my code to compile under Mac OS. So far, so good - I just need to set up GDK+ (setup SDL, FFmpeg and dependencies without any issues).