Everything on the AF phantoms were the same on the Navy jets with the exception of the rear cockpit and main gear wheels. The Navy Phantoms did not have side consoles in the rear. They did not have a rear stick. The radar antenna hand control was located on a pedestal below the inst panel. I will take some photographs of how the rear cockpit looks and post them. Also the Navy used a probe and drogue type IFR located on the right side of the aircraft, just beside the cockpits. The AF had the flying boom system with the IFR behind the rear cockpit on the back bone. The Navy inboard pylons were a different shape. I think those are included in the kit. That is about the most differences that I can think of now.
Berny
Phormer Phantom Phixer 
On the bench
TF-102A Delta Dagger, 32nd FIS, 54-1370, 1/48 scale. Monogram Pro Modeler with C&H conversion.
Revell F-4E Phantom II 33rd TFW, 58th TFS, 69-260, 1/32 scale.
Tamiya F-4D Phantom II, 13th TFS, 66-8711, 1/32 scale. F-4 Phantom Group Build.