I had a look at your file and to be honest, I don't know enough about it to see what the problem is. I did manage to find the cones in 2 of the 3 poles though.
He is a pic of a poly gear I made and roughly how I did it. The big difference was how I made the teeth compared to you in the original post picture - don't extrude them.
1. make a poly cylinder with 4 x the number of teeth for the "subdivisions around axis" and 3 subdivisions on the caps
2. marquee select 2 points, miss 2 points etc all around the edge of the cylinder (this should ensure you select both the upper and lower surface points)
3. scale the points out as required, this should make some decent looking teeth
4. scale the next 2 lots of points in from the teeth as required to create the boundary for the "cutout" in the cog
5. select the middle lot of faces and extrude the faces inwards to give you a "cut out" look between the teeth and the hub area
6. make another cylinder the diameter you want the hole to be and longer than the thickness of the cog
7. shift select the cog first, then the cylinder and do a poly boolean using the difference selection. This should give you a cog with a hole in the middle
8. For the curved cutouts (x3) I made a nurbs curve the desired shape and then used bevel plus to extrude the shape. I made the extruded shape with no caps, no bevel and ensured the output geometry is POLYGONS
9. reposition the pivot point of the curved shape to the centre of the cog and duplicate as required to get the number of shapes you want
10. shift select the cog first then the cutout shape and do another poly boolean using the difference option. This should make the cutouts in the cog flange.
The pic below has all faces with hard normals. Selecting the edges you want to have a smooth curve to and making the normals on them soft will give a much better rendered look.
Making a bevel on the edges should give a rounded look instead of sharp corners (similar look to making a circular fillet).
On the teeth you could manually split the teeth using the split polygon tool as indicated in red. If you did this to both sides of every tooth, the tip of the tooth could then be scaled in a little to make them a little narrower than the rest of the cog.
Hope this helps.......