The first question I would pose is, When was the last time the VST (Vapor Separation Tank) filter was cleaned or changed. The high pressure pump is in the VST tank. At the base of the pump is a screen the size of your pinky nail. If it gets garbage on it, it can give you those symptoms. What you are describing is typical surging attributed to the clogged screen. If you look at Yamaha's website for parts for your motor, you'll see the fuel pump in the drawing for the injector pump. The screen is part # 23 in the drawing below. The Yamaha part # is 66K-13915-00-00. When you service is you must change the O-ring gasket. There a schrader fitting on the fuel rail where you can attach a fuel pressure gauge while you're running to observe the pressure.
