Take a look at a steering box for a 2600/3600 at the link below. You'll notice that the larger diameter seal was used starting in April of 1977. This tells me that Ford increased the diameter of the steering box casting at that time, most likely due to reports of field breakage in some units.
Since the newer box would have been the service replacement for the older tractors, this is why you're seeing two different seals listed for a 2000. Unless the box on a 2000 has been replaced at some point in the past, the smaller original seal will be used.