Besides the obvious caliber difference, how do the 9mm and .40 Auto versions differ?

The 9mmx19 barrel is 4.0 inches long while that of the .40 Auto model is 4.12 inches long (photos courtesy of Jim Costanza):

 

The slide on the .40 Auto model is beefier than that of the 9mmx19 model in order to increase slide mass, thus slowing slide velocity, allowing both pistols to use the same weight recoil spring assembly, 50 Newtons or 11.24lbs. The slide of the .40 Auto version is also lacking the milled-out portion on the diagonal flats of its forward portion. The slide used on the Canadian model is the same as the other 9mmx19 slides but the barrel protrudes a little further in order to be "legal" in that country (photo courtesy of Rob Treacher):

So, at a glance, one can readily tell if a P99 is a 9mmx19 or a .40 Auto or a Canadian version.

Note that the polymer frames are identical, regardless of caliber. However, the sear housing assembly that is inside of the frame is different between calibers—the length of the ejector is different, specifically that the 9mm one is longer.

Also note that the striker assemblies used in the P99 are the same regardless of caliber, and thus interchangeable. However, the strikers used in the P99, P990, and P99 QA are different.

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