I assume on your option number 4 you mean HNL->NRT for the second leg of your trip, yes?
If so, then your choice is pretty simple;
Take one of the long haul flights from LAX to NRT (after a brief SFO > LAX flight) or transit through Honolulu to break up the flight into two (relatively) short flights. Everything else becomes secondary.
Since comfort has more of a priority than budget, I would break up the flight by going through Honolulu. OAK > HNL flight is, what, five hours? Then get off the plane in HNL, walk around the delightfully retro departure lounge in Honolulu, then get on another plane and continue another six or seven hours to Japan. Upside is that you can add your miles to your JAL membership, but I wouldn't get overly hung up on the miles at this point. JAL is pretty stingy with the membership benefits. Another slight benefit is that JAL will probably drop you off at a fairly convenient gate in Narita, so there will be a short walk to immigration. And most of the people on this flight will probably be Japanese people, and they will use a different queue at immigration, leaving the foreign passport queue relatively short - meaning the line for you to get into Japan will be slightly shorter than it would be if you were on a flight full of foreign-passport holding passengers. You've taken JAL before so you have an idea of what their economy class seats and meals are like. Regarding the meals, you would be taking two shortish flights if you go through Hawaii, so you aren't going to get fabulous meals. Probably one snack on the way to HNL, and then maybe a slightly more substantial meal on the way to Narita, but its all relative. It's all going to be slightly better than prison food no matter which flight you take. I mean, if you are sensitive to food and comfort, then any time spent in economy class will feel like time spent in an aluminum gulag.
As for details of seat pitch and legroom, etc... well, this is the sort of thing that Google-sensei can help you out with (Skytrax, etc...)