Ford has a very confusing application outline for the 4.6 V8. As far as I've seen, the SOHC engine was the "default" engine and got used on virtually every application except the Mustang GT, Cobra, Mach 1, Marauder, MKVIII, Continental, and now the Aviator. I'm not sure if it's the one used in the Navigator. So basically, prior to the Aviator, the DOHC engine was always in the "performance" cars, and the SOHC engine was in the standard cars and trucks.
The biggest difference that I was always told about the two engines is that the SOHC engine has a powerband biased towards the low and midrange, and the DOHC engine has a peakier powerband. This is why the DOHC engine is idealy suited for applications with a manual trans. And that's also why everyone that has a Ford with a DOHC 4.6 and an automatic trans. is always forced to adopt rather low final drive gearing in order to get any low-speed acceleration out of their cars.
