The result of my guitar travel adventure was actually exactly what I expected from Japan Airlines.
1) Despite business class having only about 5 people in it, I was told I could not take the guitar into the cabin.
because of "The Rules". OK. I expected that, and the rules are the rules. So fair enough.
2) Because of 1, I put the guitar in a hard shell case and put the hard shell case in a big box filled with bubble wrap.
Came in just a smidge under the rules for size.
3) At Narita the service for fragile items was excellent. The staff were very careful and procedures were careful. Fragile stickers
everywhere, special handling. Great!
4) I was not at all surprised to find in San Diego that the service fell apart. Items with FRAGILE pasted all over them and
special handling notes didn't matter a darn to the baggage people at SAN. A Japanese JAL rep at SAN assured me the guitar would be
taken to her counter, not put in with the standard luggage. I thought "Hmmm. This is America, not Japan, I doubt it.." But I waited by her
desk and...it didn't arrive, because it had gone through the standard luggage carousel process. The rep was embarrassed and when I asked about the mistake she just said "That should not have happened." Yeah, but I actually expected that to happen at SAN, hence the box and bubble wrap.
Got home and fearfully opened the box and case and..Whew..the guitar was OK.

Dear JAL - Your Narita service is excellent. The service on my flight was excellent, but SAN baggage could use a little work.