The prescribed path is documented under Upgrading. But if you expect "crazy" things in your current Moodle, that path might break, or worse, inherit those things. Starting with a fresh install including the additional plug-ins and Course backup / Course restore might give a cleaner result. Of course, nobody can say for sure, unless those crazy things were documented.
FYI: A single-step 4.1 LTS > 5.0 is not possible. See https://moodledev.io/general/releases/5.0. Or for an overview of the versions involved see http://www.syndrega.ch/blog/#php-and-dbms-compatibility-of-major-moodle-releases. Unless you are in urgent need of the new features of Moodle 5.0, it is safer to upgrade the 4.1 LTS to 4.5 LTS (one-step upgrade is possible). As 4.5 LTS runs in production, you can start testing 5.x in a test instance.