1989 and earlier engines had the 2 different inner pipes: one for 9.9hp and one for 15hp. These earlier engines had different outer exhaust housings as well. The difference there is in the exhaust outlet holes at the bottom of the main outer housing.
Starting in 1990 both models got the same '15hp' exhaust tube(inner exhaust). 1990 and later engines all got the 15hp outer housings too.
The older style engines(1992 and earlier)all had the same reed-plate. That same plate is also used on the later style 1993 and up...but only on the 15hp. The 1993 and up 9.9hp had a different leaf plate assembly but the changes were the reed itself and no shim. A shim lets the reeds open a little farther, used only on 15hp. Using a set of Boyesen reeds fixes all that. You still may need to buy the shims if the Boyesen instructions say to use them. I can't remember exactly...
If you want to buy a new leaf plate complete, buy the 9.9 unit. It is over $100 cheaper. This leaves cash in your pocket even after buying the Boyesen reeds and the factory shims. Bombardier prices the 15hp leaf-plate really high because people often don't bother figuring out the differences...but you don't have to pay that.
The carburetor is the main ingredient. 9.9hp=small carb, 15hp=large carb. Anyone who says "you can re-jet a 9.9hp carb with a 15hp jet..." has never actually tried it. That DOES NOT work. You have to find the 15hp carburetor. See the 9.9 and the 15 carbs in the pictures.
In short, upgrading the 2000 Johnson 9.9hp to 15hp is pretty easy. Mostly it's the carb. Go one step farther and install a set of Boyesen reeds. It makes one snappy fishing motor. The 4stroker in the next boat will think he left his anchor down.
After making any changes, ALWAYS do the factory linkage synchronizing procedure. "Link & synch" by the book.
I hope this helps out with upgrading to 15hp.