Do you have Geany installed? It is an IDE and editor that will probably work better for you than leafpad for editing xml files.
Any road, before you start, back up your current applications.menu. Copy it to your /home/you or rename it applications.menu-bak. This is so that if you need to restore it you can easily copy it back to /etc/xdg/menus or rename it again to remove the -bak.
The file is 659 lines long. Moderate length (not in the thousands

). It may take a while as you should go slow and careful in editing it.
For every <Menuname>***</Menuname> you change in the first 19 or so lines, you must change its corresponding entry(ies) in the file further down; i.e. its <Menu> to </Menu>. This will include <Directory> and <Category> entries between <Menu> and </Menu> for all sections. For every <Menuname>***</Menuname> entry you change, you must make the needed changes in its corresponding <Menu> to </Menu> entry. For every <Menuname>***</Menuname> entry you remove, you must remove its corresponding <Menu> to </Menu> entry.
After saving your changes as applications.menu, reboot.
Editing xml is not an easy task. It is easy to make mistakes. Take your time.