Hello,
Please provide some screenshots for better understanding your problem with categoires.
Also, if you have a lot of menu items and can’t save some menu options then you need to increase PHP Max Input Vars. By default it is 1000, try to set 5000 or 8000 for example http://sevenspark.com/wordpress/menu-item-limit
If Mega menu options won’t appear after the increasing the limit, try to disable all 3rd-party plugins.
Regards