We always recommend that you use a Fuel Tuner (EFI-tuner) combined with any of our exhaust systems. This is to prevent the engine to run lean which can damage your engine. To ensure correct air to fuel mixture make sure you follow the Fuel Tuner manufacturer's recommended settings.
An option would be a full EFI Tune with reflashing or similar. Problems with the exhaust due to the engine not running correctly are is not a valid warranty claim.
If your machine differs from the base model you may need to add another tune, turndown pipe, etc, to make things fit and work correctly.