My understanding is that the kit is a 747-200. To make it into an E-4B you add the extra parts. So just leave off those parts and you should be good to go.
One thing to keep in mind, though, is that the 747s have 3 different engine types. There are Pratt & Whitney, Rolls Royce and General Electric engines. This kit has the GE engines. What outfit does your father fly for?