The Holy Diver is more balanced and clearer than the JB. It is also a bit less aggressive and a bit more refined. When I had one, I remember I felt the lead sounds were amazing, but I felt it didn't have the bass presence and tightness I wanted. I also like the JB, but to be fair the JB works better in some guitars than it does in others. I don't think it should be in as many guitars from factory as it is, but matched better with individual guitars.
I ended up with the Nailbomb and even though it is rarely mentioned as a JB replacement over the Holy Diver, I think you should look into this. It is a seriously good pickup and pretty versatile, except that it always has a bit of a raspy edge. It definitely has a tight bottom end.