You realize doing 3D with the series is impossible, right? Well it's "posssible" but would require even a more patch-work job that'd REALLY make nitpicking, frame-counting, people's heads explode.
In 10 years, computers do the job automatically.
The art department just designs the standing sets as virtual sets in the computer, then you appoint the objects of the 2D film to the 3D objects in the virtual set and the computer calculates the rest for you (position of the camera, texturing the 3D objects and "refilming" it). At a certain point the computer is even automatically able to interpet the objects on the 2D film and apply them to the according 3D objects in the virtual set. BLAMMoOoOO: A 3D conversion in 12h done and ready to ship out! MUHARRHARRR!!!