Like most preferences, keyboard shortcuts can be set using "defaults write" commands in the Terminal. Useful if you have lots of shortcuts that you want to define, or if you have more than one Mac to set up.
However, the syntax isn't quite the same as the usual commands for setting a key to a value.
For Application-specific commands, use the following:
defaults write com.developer.app NSUserKeyEquivalents -dict-add "Menu Item" -string "@$~^k"
The meta-keys are set as @ for Command, $ for Shift, ~ for Alt and ^ for Ctrl. k in this example is the non-meta-key that you want to use.
For system-wide shortcuts, you can use -g instead of the app identifier, e.g.
defaults write -g NSUserKeyEquivalents -dict-add "Menu Item" -string "@$~^k"
Note that you'll need to relaunch the app before these will take effect. Also you can see if they've been successful in System Preferences -- which will also need a relaunch to show the changes.