I moved the nav to the right side of the screen in my theme. Only problem now is, if the last two dropdown menus on the right have sub-children (children of the children), those menus are cut off since they extend to the right and past the window.

Is there a way to make those sub-menus open to the left instead of the right?

That's probably going to require some JS changes. The JS template file is menu_popup.js.