While it looks like a reasonable attempt, it’s only looking at directly related effects. For instance, it notes that pedestrian fatalities have decreased since 1960 due to, among other things, discouraging people from walking. The effect of cars on population health would be much harder to quantify but might end up dwarfing many of the other factors.
Note that these estimates are attempts in general, not in the context of Manhattan, or downtown in any other city.
I'm not aware of any studies that attempted to estimate them in such an environment, I think that local factors (basically density of people) change the calculation substantially.
So.....even if you add it to the price of US fuel, it's still cheaper than fuel in the UK? And British cities have just as much trouble with congestion as American cities do. I guess what I mean is that if this extra money is meant to be a deterrent to driving it's just not enough. I'm not sure what the price would need to be to be honest. I've been to Portugal recently and the price of petrol is just insane - in the order of $8-9/US gallon. And yet people sitll drive, larger cities still have loads of congestion. And Portugal is very poor by European standards.