By .mod files, I’m assuming you’re referring to Maya’s module system.
You can put your plug-ins in the plug-ins folder so it’ll automatically be appended to the MAYA_PLUG_IN_PATH. Same goes for scripts and MAYA_SCRIPT_PATH.
If you want to get menus to load, you want to have a look at MFnPlugin::registerUI which you can use to register script callbacks that are invoked when the plug-in is loaded/unloaded which I’m assuming is sufficient to get your menus to load/unload with the plug-in.
Hope that helps.
As far as the selection mask stuff goes, I’m not aware of any solution for the locator. You could kind of fake it by overriding closestPoint and useClosestPointForSelection and always just return the rayPt so that it’s always closer than any other object for single-click selection. But it doesn’t get that selection priority that you would expect when you marquee select like it does with joints.