I don’t think you could change mouse actions from a plug-in but managing some shortcuts should be possible by changing the value associated to the ACCELERATOR_KEY key for all the Swing actions available in the program.
Menu items actions are accessible from [font=courier new]getHomeController().getView()[/font] which returns an instance of JComponent subclass to access to actions with [font=courier new]getActionMap()[/font] method.
Similarly, some actions are also defined on the plan and 3D view Swing components which are returned by [font=courier new]getHomeController().getPlanController().getView()[/font] and [font=courier new]getHomeController().getHomeController3D().getView()[/font] calls.