After re-reading your question. The simple answer to the cameras. Set one camera up render the animation but as image files and keep that in it's own folder. Move the camera a few degrees in the X trans and render again but save those frames in another folder.

It is really a simple trick. The hard part or should I say the time consuming part would be the converting each  frame/side to anaglyph, unless you want to spend a bunch of money. The rest would be easy. Any video editing software to put the single images to an .avi. Virtual Dub would do that and it's Free if you don't have one.

I still have not had a chance to install C6Pro on my new quad I just built or I would do some tests for you and show what I know. I need to re- DL C6 from Daz and get all the updated plugs before I can do anything Carrara right now.

I just have to much fun playing with my modo to get around installing anything else.