Q3. How do I earn FLY ON points?
A3. The only way is to fly JAL (including all the JAL-associated subsidiaries, such as JALways) using JAL flight numbers. Codeshare flights (flights with JAL flight numbers operated by other carriers) do not qualify, although they will earn regular miles.
Small correction: Codeshare flights (flights with JAL flight numbers operated by other carriers) will certainly earn Fly On points. I have flown AA's NRT-DFW flight twice on a JL-coded ticket, plus a Swiss flight from NRT-ZRH on a JL-coded ticket, and earned Fly On points for all flights. (Alas, the Swiss code share does not exist anymore.) But you have to be sure that your ticket has the JL code on it. If you purchase an AA ticket, for example, you will not earn Fly On points (though you will earn regular miles).