I read your STEP file into SpaceClaim. I combined all the bodies back into a single body. On the Repair tab, clicked the Inexact Edges tool.

It found six, but could only repair four.  Two inexact edges remained. This may cause problems meshing.

Also, I can't remove this extra face.

Precise geometry is needed for easy meshing. Inexact edges are going to deliver poor quality meshes as I found in this trial below.


It might be worth building this geometry from scratch in SpaceClaim. I did a blend instead of a chamfer and used a sphere to slice out the joint.  The parasolid file for that is attached in the zip file.