Mapping Super Keys to Control without Xmodmap

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http://unix.stackexchange.com – I've been attempting to switch my super and control keys in X on a macbook and have been half successful. I'd like to avoid creating a custom .Xmodmap if possible, as there is a temporary 100% cpu bug that pops up every time the custom map is loaded (not to mention various warnings against using xmodmap generally which I've come across). After some diging, I ended up putting Option "XkbOptions" "altwin:ctrl_win" in my 01-keyboard-layout.conf file which has gotten me halfway there: for eg, left command now maps to 133 Control_L. However, the control keys remain the same. Left control, for eg s (HowTos)