Hello twofoot,
Your surfaces are skimming one another in a few instances and you happen to have little surface slivers in other cases which are preventing the surfaces from joining into a solid. In cases where I find surfaces not fitting together I step back and try to see if I can model the solid using more of a different command set. In this case I would use more Boolean operations using curves to prevent the surface skimming sort of issue you're experiencing.
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