Answers from the mailing list of Aquamacs:
1.
Pretty much all key bindings in Aquamacs are bound in osx-key-mode-map (see Aquamacs FAQ). The mouse button bindings aren't any different.
Press C-h k, then the right mouse button (over an Aquamacs window). This should bring up a help screen that explains that this key is called `down-mouse-3', and that it is bound to a function described as this:
(osx-key-mode-down-mouse-3 EVENT &optional PREFIX)
Activate context menu, when osx-key-mode-mouse-3-behavior' is
set to
aquamacs-popup-context-menu' or nil
Looking up the documentation for this customization variable doesn't bring up anything useful, but we can undo the key binding (see Aquamacs FAQ, probably) using define-key:
(define-key osx-key-mode-map [down-mouse-3] nil)
2.
There is a second approach in place to return mouse-3 to its vanilla Emacs behavior:
In the Aquamacs help/manual, section 4.3 "Customizing Aquamacs behavior", under "Want some GNU Emacs 23 behavior back?" there is a list of Aquamacs-specific settings that can be customized, including "OS X Key Mode Mouse-3 Behavior". Try customizing that setting as described in the help -- that may allow ECB to behave as in vanilla Emacs.