[n4mwd]

The intake, carbs, headers and exhaust are so precisely tuned on a Ninja that any tinkering with the design can mess things up. If you change the mufflers to a single muffler, or airbox to pods, then that generally means rejetting the carbs. If someone changed any of that stuff, and didn't rejet the carbs, it might cause the bike's performance to suffer in a manner similar to what you described.

So if you have a stock bike, it should have two mufflers, an airbox and an oil sponge air filter. Based on what you have said so far, it sounds like this is the case.