OK I have looked at the file, some points to note:
There were 608 duplicate vertices in your mesh - not good! :no: - select all vertices, then key w and select “Remove Doubles”. These will cause you performance issues.
You have some topology issues to fix - like misshapen parts, insufficient vertices around the curves. These you can work on once you have the rigging correct.
You have some faces that needed “normalising” In Edit Mode - Ctrl-N to fix these, this is generally caused by mirroring faces, which then are no longer “External” to the outside of the object, causing them to appear much darker.
You have no lamp - so it will never render - I have added a sun.
You have no camera - so you cannot do other than render preview.
Your Render settings were 1080 wide by 1920 deep - they should be the other way round.
Your background was black - not good to see things against, particularly with no lighting! You will find a sun and a camera on another level.
With a sub-surf modifier, alway check the “Optimal Display” box, or it can be very difficult to see through the object in wireframe mode. I always put the Armature Modifier AFTER the sub-surf, makes for better animations, others have disagreed with me on this point BTW.
You have removed the Armature Parent setting for the assembly, but still had the Armature modifier and Vertex groups. If you want to connect a new armature, Remove the Parent, Delete the Vertex Groups, Remove the Armature Modifier, then start again with your new armature, and parent the mesh to the Armature first, then do the vertex assignment.
Your IK constraints are all wrong, but as you don’t need them I will not overload you with why. When you do need an IK, let me know and I can help. The flip on the bones was as I thought in my previous post.
But, I have fixed your file for you, you will find the new stuff on two other levels from yours.
Frag_Hydro.blend (1.5 MB)
Just run the animation (Alt-A) to see it working, then you can take it to bits to see how it works. Move or rotate the “low-couple” bone to operate it yourself, or you can rotate the “top-couple” bone as well.
Have fun, the initial learning curve with Blender can be VERY steep! But we are here to help. :yes:
One final point - you may be better off having each separate part of the assembly as a separate mesh - it makes for much easier vertex assignment in mechanical system. You can separate them out by going to Edit mode, selecting all the vertices associated with a particular bone from the Vertex Groups panel and then keying p - and chose “Selection”, this makes a new mesh of the selected vertices.