Great info Daniel.

I use the free software over here:  stereo.jpn.org/eng/index.html (Also for batch and movie processing! )

As for the camera and focus, i have made my default start scene equipped with stereo camera's.  Now when i move the  main camera around, the left and right eye automtically follows. Only be carefull when changing "focal" .

I will link this file as a .txt, maybe someone find it usefull, i connected two extra cams to the main camera, a few cm apart and with a 6 degree difference.

This way i am able to work as normal and with the switch of the camera instantly produce a left and right view from my main viewpoint.

As for youre 20 renders problem.  Try this:

Just take one camera, aim it at you desired focal point and set in the animations tab : Track > (choosen object)  , you can hide this object if you want.

Now turn on animation and make the animation path of the camera move from the left eye to the right eye position.  (Due to the track function you're focal will stay correct! ) 

Now you can render the animation with single file output and you will have as many "frames" as you wish with one push of the button!

(You could save this camera setup maybe as an animated VOB so you can load it in any old scene as well)

Rob