Almost every menu command which can be executed with the mouse can be run from within a script. (Menu Commands which require typing or which product a choice-list cannot be run from scripts.)
The script command is: activate-menu-item <command>
where <command> is one of the following list:

In order to remove menu items, please use the following command:
remove-menu-item <menu-item>
For example:
remove-menu-item Setup
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