On with the task. If you want to change or delete Main Menu items as root, 'cd' to /usr/share/applications and do an 'ls'. You will find each Main Menu item as a single entry ending in .desktop. Do a 'cat' on one of the files to see its contents.
# cat lxterminal.desktop
Comment=Use the command line
Each is a text file containing a description of which commands to execute, type of application, icon and language. (I didn't include language description. Too many entries to list).
To remove a Main Menu entry, delete the file.
# rm lxterminal.desktop
To change the location in the menu system, change 'Categories' to a different type.
Most entries are self-explanatory:
Encoding: The encoding used to display the entry
Name: Name you see in the menu
Comment: Comment you see while mouse hovers on entry
Exec: Command to launch application
Icon: Icon displayed in menu
Type: Application type
Categories: Where its displayed in menu system
LXDE automatically lists entry names alphabetically and updates the menu entries when they change. If LXDE does not update your changes, as 'root' do:
If you need to change icons, they reside in /usr/share/pixmaps. You can dump new icons in the directory or choose others already there.
You can check details with xdg-mime. Take a look at the man page: