Open the geometry in SpaceClaim. On the Workbench tab, click the Share button. You should see all the edges that touch, highlighted to show they will be shared. After you click the green check mark, edges will be color coded for how many surfaces are sharing each edge.

Open the model in Mechanical. Most of the bonded contact is no longer needed so delete that. There may be only a few areas that need bonded contact or a Fixed Joint.