Building a quasi-3D Blu-ray for "An Ancient Pond"

So I'm using my first of three thesis projects as a guinea pig for packaging all of my 3D movies so people can enjoy this 3D goodness in the comfort of their homes.  I'm currently transcoding the Blu-ray image for An Ancient Pond for burning to a BD-R on campus later this week.  Since I don't have access to a true MVC Blu-ray 3D encoding suite, I'm going with the next best thing.  An Ancient Pond is being encoded on the disc in three different formats:

• Left eye only for folks without a 3DTV setup and no desire to use anaglyph glasses
• Red/Cyan anaglyph encoding for 3D fans who have a 2DTV
• Side by Side squeeze for people with a 2nd generation 3DTV than can process SxS media

This was you can choose your method of viewing and have a 2/3 chance of doing it in stereoscopic 3D.  Ideally I'd be able to encode in full resolution MVC, but that'll come later.  I have a thread over on Creative COW asking people about how to best achieve this without forking over $4000+ for the MainConcept MVC encoder.