I checked JL 3 menu before Covid-19 suspended the flight.
For first class, there will be both the typical main meal and then a la carte snack menu and two set plates - one Japanese and one Western.
The timing of the meals will be flexible

For business class, the main meal will be served eight hours after takeoff (don't ask me why). If you check the current business class menu on JL 41 with a similar late night/midnight departure and early morning arrival, you will see the similar offering.
https://www.jal.co.jp/inter/service/...206_202208.pdf

Unfortunately JL 41 is a 787-8 flight now, so no first class menu. But given the much longer flight on JFK flight, main meal service will be offered unlike the "shorter" SFO menu. Plus JAL offers a "lounge" service for F/C/PE passengers so they can have a full dinner prior to boarding the flight to JFK and Europe to maximize sleep. It is clear that not offering a full dinner on these midnight flights is not working, or the flight goes much longer now without access to Russian airspace, so not serving a full meal is not an option anymore. But thankfully JAL will post the menu online once they are available. So you can always check then.

Carfield

PS. Regardless just be grateful you are not in PE/EY, they only get one full meal service on these 13 hours flight from Tokyo to London midnight flight now. They serve the meal 8 hours after takeoff and that's all. No real breakfast or real snack...