Baz, I suspect your absolutely right regarding the directional compass atop the instrument panel shroud, being a post-factory/in-service modification. In a 1970's era photo of the Belle's cockpit, that gauge and bracket are long gone, but then in a collection of photos of the interior restoration of the aircraft as of 2009/2010, the bracket for the gauge is fitted again.
Right now, at the USAF Museum, they are waiting for the interior restoration of the Memphis Belle to be completed before they paint the exterior. Last I heard they expect it to take up to two more years to complete the restoration.
Another cockpit detail I've picked up on over the years is the communications radios used in the B-17's in England. Usually the B-17 cockpits are always modeled with the standard/factory-type installation of the SCR-274 radio set, as would have been used State-side and in some Theatres like the CBI. However, in England, the SCR-274 set wasn't fully supported, and the VHF SCR-522 radio set (British TR-1133) was the only standard/norm. Rather than the BC-450 control box (SCR-274) fitted to the ceiling of the cockpit (you can see it removed in the photo of the cockpit of the Memphis Belle, with just the mount/plugs remaining), a BC-602 control box for the SCR-522 was attached to the left of the center console, in easy reach of the pilot. All bombers, fighters, and troop carriers flying in and out of England required this particular radio set, and it also became the standard VHF set in the Pacific as well.