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Install files only get pulled into Drupal's active code on very rare occasions, so unless you've a specific architectural reason for splitting them into other files (e.g. you're going to need some, but not all, of your code in some other code elsewhere) then I simply wouldn't do it. All in one file, but make sure you follow Drupal coding standards and comment functions properly with docblocks.

What you describe shouldn't involve very much code anyway. Any reason for not using features? This is the standard way to create content types, views, taxonomy vocabularies etc. and it handles its own file-by-file separation. It would make most of the separate files you mention go away, I think.