1. I don't think you'll get priority boarding. There won't be anything indicating you're a priority passenger on you CTS-NRT boarding pass and your NRT-JFK flight in J is irrelevant to your boarding status at CTS. However, you can enter the ANA Lounge at CTS since you'll be transiting to international J later.
2. Yes. You should check in for your NRT-JFK flight at CTS. The domestic counters can check you into your international connection. You should use the ANA Diamond/Platinum/SFC/*G counter at CTS and all should be easy peasy.