You can not change the order of Tool menu items which are predefined. But you can change the order of items added by you.
Custom menu items appears in the sequence in which they are assigned in cell array in the definition of custom menu function.
% Register custom menu function.
function sl_customization(cm)
cm.addCustomMenuFcn('Simulink:ToolsMenu', @MyMenuItems);
end
% Define the custom menu function.
function schemaFcns = MyMenuItems(callbackInfo)
%------You can change the sequence in the below line------
schemaFcns = {@getItem1,@getItem2,@getItem3,@getItem4};
end
