Thank you for the image.  I would like to know what the hooks are attached to above the top edge of the image. If you can show more, that would be helpful.

Is there a chain tensioning mechanism?  If so please describe it. I believe the lowest frequencies in this assembly are going to be the motion of the chain links.  The tension in the chain will have a large effect on the frequencies. If there is a chain tensioning mechanism, then you must have a Static Structural analyisis to Pre-tension the chain, and you link the Solution cell of Static Structural to the Setup cell of the Modal analysis in Workbench.

Modal analysis is all about stiffness and mass. It looks like the structure has a base that is fixed to ground, perhaps at four bolt holes that are not visible in the image. Use a Fixed Support at the bolt holes. If there is a large mass at the other end of the structure or the hooks, that mass must be represented in the model. Again, what is above the hooks?  A significant amount of mass I would imagine.

Create a Revolute Joint between the shaft and the bearing to leave the rotational degree of freedom of the shaft free. 

Delete the chain solid body and replace it with a Line body in DesignModeler, or a Beam in SpaceClaim. Now you can mesh the Line body/Beam with Link elements.

Each line body connects to the sprocket at the tangent point with a spherical joint and to a hook using a spherical joint.  What supports the hook, I don't know.

If you don't care about the vibration of the chain, just mesh the line bodies with one element each by using a Mesh Size control to force that to happen.