Hi Sebastian, you can get rid of a bunch of the naked edges by just selecting your object and using Edit > Separate followed by an Edit > Join, that gets rid of about half of the unjoined areas, but there are still 11 edges primarily on the outer shell that are not joined (use the script shown above in Andrei's post and also described here to see them:
http://moi3d.com/forum/index.php?webtag=MOI&msg=6051.2 )
When 2 pieces do not join together, it means their edges are more than 0.005 units apart from one another, so that's kind of an indication that the surfaces are not all that accurately hugging one another.
If that accuracy problem does not bother you, then one quick workaround is to scale your model down (which also reduces the distance between edges too), then join, then scale back up. If you do that in this case you will be left with only 4 naked edges on one surface so you can focus on rebuilding that one surface.
So that scaling rejoin sequence goes like this - open your file, select the object, run Edit > Separate to break it into individual surfaces. Run Transform > Scale, and at the first prompt that says "Pick origin point" type in 0 and push enter to specify 0,0,0 as the scale origin. At the next prompt that says "Scale factor", type in 0.1 and push Enter, your object is now scaled down by 1/10 in size. Now do an Edit > Join, and now repeat the scale this type using a scale factor of 10 to scale it back to its previous size. Now use the select naked edges script to see the 4 remaining naked edges that bound one surface - the actual problem there seems to be that there's a duplicated surface in that spot so it's not able to get a clean join in that location. Delete one of the duplicated surfaces from there and do one more Edit > Separate and Edit > Join and that will get you a solid with your existing pieces.
But like Andrei writes above, it is generally better for things like this to be formed by a single taller simple cylinder piece that is then cut, rather than trying to directly loft a surface between the bottom edge that is curved in the z direction with the top, that kind of direct-to-irregular-edge surfacing has left some ripples and bumps in your surface that you may not really want:
But anyway that sequence above can be used to get a solid out of your current object just as long as you don't mind that some of the surfaces are not touching each other to a very high degree of accuracy.
- Michael