I can't recommend the SU solid plugin enough.
http://www.susolid.com/
It does cost a small amount but I don't think I could use SketchUp for solid modelling without it.
Using it it took me about 30 seconds to make the file manifold.
1. You have one group and the rest ungrouped. I exploded the group, selected all and grouped the lot.
2. Run 'analyse' from SUsolid which highlights problems in various colours. Yellow means internal surfaces (screen attached).
3. Double click to edit the group, then right click and hide several of the external surfaces. Delete offending inside surfaces (mainly flat 'discs') (screen attached).
4. SUsolid can be run even when faces are hidden. Here we see the dialogue says solids = 1 and the shape turns purple. Manifold! (screen attached).
5. I have an unhide all plugin to bring back the hidden surfaces. Part finshed! (screen attached)
Post's attachmentssusolidprocess.jpg
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