Keith, I've responded to your post on my blog at http://libertyscott.blogspot.com/2008/05/abandon-railways.html
The simple point is that long distance rail and road freight have similar environmental impacts on a NTK basis on average, with both varying according to route. Road is higher overall because it carries all short haul freight, and most environmental costs of road (and rail) freight are in urban areas. Most short haul freight is within metropolitan areas, so the exposure to people is, on a Net Tonne KM basis higher than rail. The Surface Transport Costs and Charges study, which is available from MOT direct (sadly removed from its website) clearly states that the marginal environmental costs of rail and road freight are similar for freight between Napier and Gisborne, rail is higher than road for Wellington to Auckland and road is higher than rail for Kinleith to Tauranga.
You've quoted poor quality data, a European study which is not comparable (far higher rail freight capacity and volumes to get economies of scale) and Chris Kissling who frankly isn't very credible at all, given he waxes lyrically about the future of transport including "smart clothes that open doors for you" (does he live in a cave to not notice electric doors aren't new?).
The environmental case for rail is very slim at best, at worst it's a fraud and rhetoric by those who worship rail as a religion. I personally love trains and know a great deal about rail, but I'm not going to pretend rail is what it isn't.