arXiv preprint and final paper differing by sections and appendices
There doesn't need to be a strict correlation between an arXiv publication and an actual publication. It's actually common to use arXiv to publish extended/longer version of a published version (which seems exactly what you want to do). So 


Yes, it's OK to have a final paper that differs from the arXiv version.
Yes, it's even encouraged to cite the arXiv version to point to appendices/extra material/proofs/detailed examples, etc. 


However, the main rule is still that your journal paper must be self-contained, i.e., must be understandable without having to read the arXiv version. In other words, if removing the section implies to remove a definition (for instance), then you must put this definition somewhere else in the paper.