some important notes on cleaning up non-manifold geo. first of: know what is causing nonmanifold geometry!

look at the maya docs, there it says:

a) three or more faces share an edge.
b) two or more faces share a vertex but no edge.
c) adjacent faces have opposite normals

what does that mean?

1) it does not mean you must have all quads or tris or 5sided. you can have whatever n-gons you like (til 255 or something like this). n-gons wont cause nonmanifold geo.

2) your mesh must not be watertight but can haver holes if the topology follows the above rules.

3) in most cases it´s the normal thing. I´ve overseen it a hundred times, searching for hours n hours. so check your normals and make sure the all stick at the same side of your topology.