I went the opposite direction back in the day on my track car.. I started with a 3.0L big port SC motor 8.5 to 1 with SSI's. I had installed a 3.2 Carrera intake with programable FI on the motor for more power. I tuned this the best I could on the dyno and it did make more power. I then decided to back to stock class and reinstalled the factory CIS. The dyno below shows the difference.
You can see the CIS does a little better from 3.5K-4.5K RPM. From 4.5K up the 3.2 manifold is much better.
I eventually rebuilt the engine and installed later 9.3 to 1 pistons with the CIS and got much better power with a fresh engine and more compression. I would have liked to run the 3.2 manifold with the rebuilt engine but never did. Dyno below is my car and another in my class with same build specs. 3.0L big port, later 9.3 pistons, headers and good exhaust, advanced cam timing and good flowing muffler.
I would expect to get 20HP+ with a better intake system.
john