It is too bad the only west coast direct flight with JAL to KIX is from LAX. If it were SFO we would do it, but LAX is so inconvenient. We did that when we flew to Australia a few years back—-I scored tickets in First on Qantas with our Alaska miles. But it made for such a long and tiring and expensive trip (overnighting near LAX, not much fun for us) that we decided not to do that again.
I think the best option for us is the direct flight from SEA to NRT and overnight in Tokyo, then the Shinkansen to Kyoto the next day. We did that in 2019 and it wasn’t a bad way to start our trip. I was just hoping to fly to Osaka this time, and it seemed possible earlier, but the schedule change has made that an unattractive option.