Ashley,
I'm sorry to bother you. Would it be at all possible to add plugin properties to the config.xml file for phonegap exports? For example the app id and app name listed below.
<gap:plugin name="com.phonegap.plugins.facebookconnect" version="<VERSION>">
<param name="APP_ID" value="<YOUR_APP_ID>" />
<param name="APP_NAME" value="<YOUR_APP_NAME>" />
</gap:plugin>