You will be on a separate booking reference.

I think BA can link two bookings together to allow a status cardholder on one to trigger free seat selection (or the call centre selects them manually). I think only Golds tend to get this, though, and it is not guaranteed at all.

JAL availability should show on ba.com if there.

We have done numerous CW flights with adult on the end of the middle block and 2 kids in the 'double bed'. It works fine as you can reach them easily. Any middle block of 4 is fine. Even if you don't preselect, people are happy to move around onboard. The 3 on the same PNR will be sat together anyway as BA is not allowed to separate kids from adults. And no adult wants to be sat facing a 3 year old for 12 hours .... people will be queuing up to get out of your way.