For JP to state that it caused a loss in HP is just stupid. Even highschool mechanics students know that an engine is like an air pump. The better an engine can "breathe" the more efficient it will be. They wouldn't spend the money to redesign the manifold if it wouldn't change the power output and make up for the more restrictive exhaust.
OK, so please show us your documented proof that the 99 intake flows better and makes it breathe more efficiently. Maybe they really did lose HP. It is entirely possible to lose HP and make more torque. Every "highschool" mechanic should know that also.
I wait for your documentation to show that their report was "stupid".