Take any of the morning nonstop Nagasaki-Haneda flights (ANA departures at 08:35, 09:25, and 10:55; also some JAL flights available), then the limousine bus from Haneda to Narita?

In principle it could all be done on the train, but it's a looong day on the rails: an 06:00 departure from Nagasaki Station can get you to Narita T1 at 14:57. I think you're losing out on the "easiest" and definitely the "most convenient" at that point - its only advantage is that it's cheaper than a standalone NGS-HND flight. Perhaps you can add that segment to your existing NRT-SFO ticket for a more reasonable price?