I was trying to clean my parts storage and ran into two airboxes and took a couple of pictures to illustrate the difference.
As you may see in the first pic, the carb connections in the Prolink box (top) are sitting a tad higher than on the early box. This may not necessarily mean that it is an issue, you may still get the box on the carbs.
However, if you then want to line up the airbox with the filter housing, you may have trouble as the second picture shows. The height difference between the carb connections is quite different when the filter housing aligns.
You can also see in the first picture, when looking through the carb openings that there is a larger portion of the back filter housing visible on the Prolink box.