i can answer some of your questions and people who know more will help you out as they see this thread.
yes aftermarket pipes will give you extra power and can change where the power band is on your buggy(or any engine). It will also have a different sound.
What do you mean by rubber manifold? picture? Is there a metal piece that attaches to the motor and then a rubber one that connects that to the pipe?
also for a different view you can check this thread out:
The right pipe