Richard Tanner's book 'History of Air-to-Air Refuelling' has no mention of the F-111 at all. It has various other projects and plans, which I've posted elsewhere, but nothing on F-111K. That may mean that Flight Refuelling Ltd. wasn't behind the changes, or simply that the author left such work out (although it seems a pretty through work with Jaguar M and H.P.99 included etc.)
One thing that's gotten me wondering is how well an F-111 would refuel behind a Victor tanker? What would the clearances be like and the tanker efflux? Perhaps that is the reason why the wing-mounted boom was replaced by a nose boom? I assume some kind of testing would have been done at some point in the programme (perhaps once the prototypes were flying) but all American tankers had wing-pod engines while those of the Victor are close to the centreline. Single-point refuelling would be the only option I think.