We got a response from the 'yakuba' (town officials) and after discussions with both the mayor and deputy mayor, it has been agreed that we can both (my wife and I) apply to the rural cooperation scheme (協力隊).. which is great news. Apparently this essentially means that we have been accepted and the application and subsequent interviews are just tickbox exercises!
I'll wait until after we've officially applied and officially been offered positions before I drop the bombshell on my current employer though.