According to the asiamiles website,

"2.You can make a maximum of five stopovers, two transfers and two open-jaws at either origin, en-route or turnaround point, subject to airline partners' terms and conditions."

So your NRT-LAX, LAX-BOS will count as a transfer, not a stopover.

One hint: you can use a stopover as a transfer. I've had to do that once, when I had 4 stopovers + 3 transfers. They counted one of the transfers as a stopover to comply with the rules.

No idea about your JAL problem. Book AA instead, just so that you don't have to worry about it.