A lot of pipes, such as the Epco Stainless ones, come with a set of jets if they are needed.
Once the pipes are installed, start the bike up and let it idle a little bit to warm it up. Then, open the throttle and see how it runs. (don't hold it open more than a few seconds!) If it starts missing, it is certain that you need to rejet.
If the exhaust pops excessively on deceleration, it could mean that your idle mixture needs to be readjusted. Adjust for highest idle speed. If the idle mixture scews end up out more than 3 1/2 turns, you probably need a bigger pilot jet.
Popping could also mean that you need to add some high temperature sealer to the joint where the mufflers connect to the headpipes because fresh air leaking into the system can cause that. Which gets us to another thing that you will probably want, this kit
http://www.newspeedmaster.com/html/ai_removal_kit.html to stop air being injected into the exhaust system on purpose. This is done to reduce emissions a little by burning any excess fuel before it gets out into the atmosphere. Unfortunately, burning fuel in the exhaust system heats the pipes up to the point of damaging the finish.
By the way, poke around the newspeedmaster site a little if you dare, you
will wnd up buying stuff!
