Changing icons in E menu's is easy, if a little time consuming.
In your ~/.enlightenment directory you will see all sorts of menu's. The one called user_apps.menu is the top menu with your apps in it. Open it in an editor.
The first item on a line between " " is what you will read in the menu, usually an apps name. For example "Firebird" for my browser.
The second item between " " is the path to some icon you will see in your menu. You should change that to whatever icon you wish to see there.
The third item is the word exec.
The last item is between " " again and is the command to execute.
I am not aware of any tools that will do this for you, but that doesn't mean they're not there.