I'm tempted to say, put one lens in autofocus, the other in manual. Run something like a large o-ring or fine tooth timing between the two focusing rings, depending on friction and perhaps a few small dabs of tap or gummy stuff to avoid slippage. Hope the lens in autofocus has enough spare torque to drive the lens in manual focus. The elephant in the room is that on autofocus lenses the focusing rings are a slip-fit to the actual focus mechanism, so an out-of-sync situation is not only possible but likely. Constant checking is advised.
Another possibility is to use a pair of selsyn motors to transfer the autofocus lens's position to the manual focus lens. Not recommended.
Very difficult to get large camera bodies spaced at the normal eye space distance, especially with horizontal orientation. Cameras with normal focal lengths spaced too far apart exaggerates the 3d effect in bizarre ways. Having one of the cameras looking sideways at a 45 degree, front-surface mirror right next to the other camera's lens is one complicated possibility to close the distance. It's easier with telephoto lenses, because in that special case you actually want rather large camera spacing (interoccular distance) to create a 3d effect with an apparent convergance point much closer to the subject than the camera location.
If you are shooting movies, you will need to have some way to control the convergance point, which is the point out in front of the cameras where the optical centers meet. This is kinda-sorta roughly where the audience will perceive as the location of the black frame around the image. If you get the convergance point wrong, bizarre effects show themselves, as in the case where the convergance point is farther away than the main attention-grabbing subjects in the scene. That forces the image in front of the black frame, or "proscenium." That's how you get the "jumping out of the screen" effect, just be careful the jumping out subject does not get clipped by the edge of the frame for very long. Did a lot of 3d work in my movie days, the process imposes a lot of constraints and it was never easy.