The Art1OptoFix piece is no longer needed if you printed de latest version of the BaseBot piece (which I think you have printed) and you are going to use the commercial Optical Endstops listed in the BOM.
I’ll note it to remove the piece from the repository ASAP.
The Art4BearingPlug piece is used to prevent the bearing balls to escape the ring. In the assembly animation it should be inserted in the same hole used to insert the bearing balls after inserting them. This video of Sr Ferrete shows how he inserted the balls and the Art4BearingPlug piece.
The Art56Interface is only needed if you want to use other tool than the Thor Gripper. This piece provides 3 screw anchor points, and can be used as a base to design your own tool holder.
In this image you can see a Thor using this piece to attatch a different gripper.
Hope it helps!