What is the age of your lens? I have several friends here with 500 f/4's, I don't think any are VR versions, I will contact them to test. Remember that there are electronics in both the lens and the camera. It may be that the lens will require a mod as well as the camera. For example, I have a 400mm f2.8 AFS-1 which reports focal lengtj correctly when used with the 1.4 and the 2.0 TC',s but not with the 1.7TC, it reports that focal length as 950mm. The lens is so old that Nikon will not rechip to work correctly with the TC.
Point being, be sure to let Nikon know lens age as well. Do you have a local store that may have a newer 500 f4, non-VR, that you could test with?