Don't need to worry about that. I have no plans to visit Japan anytime again in the near future. I'm planning for Holland, if it works out.
I'm sure JAL can accommodate that unless they changed their system. I used to fly JAL to Narita then transit to San Francisco. The first day stayover at a Narita hotel was only US$25 extra arranged by JAL. If extended more days, then pay the standard hotel rate, and what hell, you can choose your hotel since you're paying full rate. Of course that time, I made full use of the first day stayover offer and then went to stay in my GF's home. The Narita area isn't bad actually. Very good and inexpensive Japanese food around the Narita Eki (station). Relaxing environment good for strolling around. Trains to Tokyo is within 30 minutes.