Thanks all - I ended up taking the plunge on Monday. It seems like $3500, at a minimum, is a pretty decent price for JAL (or another non-Chinese carrier).
That said, I did see today that AA is doing a super cheap 45-55K per direction saver ticket to Japan right now. Anyone else looking at this should consider that, even if like me you don't have the miles, as a quick peak shows you can buy 185K miles (enough for two tickets) for $3,208, so $1,600 per ticket. While in my case, I'd still need to get TYO -> SIN, probably another $800 each, that'd still be a substantial savings at $2400 total per ticket vs. $3500.
Painful to see that now, but I'll live... at least I'm earnings miles on the JAL flight, which I calculate at 22.5K redeemable miles, 45K status qualifying miles on American, and $5.6K qualifying dollars. Enough to get me into their bottom tier with one flight, and likely their second tier with another flight or two.