I would do option 3 if I could arrange for early check-in at the hotel in Tokyo to freshen up. You can sometimes get a 6 AM check-in if you agree to pay for the night before although some hotels might not allow this. Of course, the main point of the early check-in is to shower and change clothes; you don't want to sleep any more than a very quick nap right away as it will wreck your sleep cycle.

I did the ANA LAX-HND run a couple of times last year (basically the same schedule) in PY. Had dinner and a few drinks in the lounge, showered and changed into comfortable clothes, then boarded the plane and conked out shortly after takeoff, dozing through most of the flight. After getting home first thing in the morning, I played with my kids until lunchtime, then took an afternoon nap for a couple of hours, and was right back on Japan time after that.

As far as the departure time is concerned, I took a midnight flight to Hawaii from HND with my 2 y/o daughter last year and she had no problem staying up until midnight out of sheer excitement (but promptly fell into a deep sleep once she was strapped in on board), so it may not be as much of a problem as you think.

One trick that I find to be helpful is to switch to destination time as soon as you can (preferably on the day of departure) and do your best to eat and sleep on the destination time schedule. Dinnertime in San Francisco is close to lunchtime in Japan, so consider having a lunch-like meal at dinnertime on your day of departure, followed by a dinner-like meal late at night (either right before or right after departure) and some breakfast before landing if you are hungry. Try to sleep though overnight hours in your destination time, and limit sleeping outside that window to short naps in between meals, movies, etc. This is easier to do if you're flying in a business class product where dining is on demand.