It's very likely things will break or perform differently between both the contrib plugins and the custom, plus themes and menus. 

If you've got a big course that uses all the plugins you like using across all (or you can throw one together) it may be helpful to do a preliminary export of this master course from the old => import to the new, assuming you've got access to both instances concurrently. 

This process will help you understand and document what needs to be replaced and tested once all courses come across.