That popping sound (kinda a mini backfire) is from the fuel to air ratio being too lean. Only replacing the muffler (on a bike or car) reduces the backpressure. The engine breathes out better. When you allow the engine more air in, via a performance air filter, the engine breathes in better. Now, you've got more air, but less fuel. Hence it being too lean (air/gas mixture for combustion.) Get it remapped or jet it to put more fuel when the engine needs it.