The paths to these files look like they have been updated in our implementation. Are you currently experiencing any errors in your live page in regards to these references? I have not seen any issues in regards to these files so far.
If you would like to update the paths these files should be in the kfm/includes/pear/ directory, you can update them like this:
include_once 'includes/pear/MDB2.php';
If you are not having issues with these values on your app though updating them may not improve the functionality and could possibly make some things not work. In my testing I did not get an error after updating paths. Let us know what you encounter.