Old Ford Syndrome is a very real affliction

Trust me; I've got a '77 Ranger with a 460.
Ok then: how does air enter the engine? On most vehicles, there's a single air intake somewhere that feeds into a chamber (the plenum) atop the engine. Typically, this part of the intake is more or less a common area to all cylinders, but not necessarily always. Since I don't know offhand how 4.6L Ford was designed, I thought I should make sure.
Fuel rails exist on port-injected engines. They're basically hollow pieces of metal that the injectors tap into, and all they do is feed fuel to the injectors. They look just like a metal tube running the length of each cylinder bank. Every port-injected system I know of is considered to be "dry", where fuel is added to the intake charge only as it enters the cylinder.
Throttle body injection (TBI) moves the injector(s) to the throttle body itself. This is considered a "wet" system, as the fuel is added to the engine as soon as air enters the engine (carbureted engines are also wet).
If you've got four clean plugs on one bank and four dirty plugs due to carbon deposits on the other (which sounds like that you describe), then the side with fouled plugs is receiving too much fuel. That's why I'm wondering how air and fuel induction is being handled with your engine.