My bike had the factory race kit on it when I bought it. Muffler, ECM, and filter. My air box had also been cut.
I just replaced the filter with a K&N, did the breather re-route and NGK plugs. The bike runs/sounds great.
There are a lot of threads about cutting the factory muffler. Do you want to keep the exhaust servo ?
Just after a better sound or more performance? Depending on what you do, you'll at least need a tps reset. Might need a full tune.