Now its a good idea to choose the mesh aglomeration with the fewest partial meshes.
Group the meshes of this aglomeration as Group A and all the rest as Group B. Align Group A to B:
Same procedure with the next aglomeration: Group all members, Group the rest Align A to B:
If there's no aglomeration left to align ungroup all and do GlobalAlign:
No need to think about which partial scan matches to an other mesh.
Hope that helps a bit