Motorcycles are tuned at the factory to run with the stock breathers and exhaust pipes. any time you change a component, breather or pipe, you change that setting. if the change is minor, such as changing the pipes, or the breather to a more open configuration, re jetting the carb may not be necessary. when both are changed, the gas-air mix becomes too lean, and the bike runs poorly, usually backfiring out of the carb. this is when the re jetting needs to be done, to allow more gas to the engine. usually the slow jet, or smaller jet will be replaced and sometimes the high speed, or main jet is also replaced.
on fuel injected bikes, the computer system will have to be re mapped, or re-programed, since these fuel systems don't have jets. or carbs.