It's a two hour ride from Nagasaki to Hakata (Fukuoka) on the limited express. Not a true shinkansen yet.

Are you flying UA? Could you possibly get a return on the KIX-SFO flight instead? There's still no useful connecting flight out of NGS (the one daily flight on Peach arrives too late), but it is at least a little more reasonable by train - just under six hours from Nagasaki to Kansai Airport, instead of nine to Narita. Nice airport, too.