You can use Moodle's "Language editing" feature to edit the help files (and other lang strings) through the admin screens, without directly editing code files. In the Moodle admin menu, go to Language->"Language editing". The documentation is online here: http://docs.moodle.org/en/Language_editing
I think the most you can customize the Moodle Docs links is to go to Appearance->"Moodle Docs", and there's a setting that lets you change the domain name that is used for Moodle Docs. You could probably point that at one your own servers where you keep your own custom Moodle docs, and set it up so that if you don't have a custom doc for a given path, it redirects to docs.moodle.org.