You will have already been in Japan for well over a month. I would strongly recommend just getting your butts to NRT in plenty of time to avoid stress or potential problems with making your departure. Rather than trying to squeeze in "a few more hours," consider that Nagasaki is a long way from NRT and act to ensure no snags along the way.

I have made an easy departure from Fukuoka to KIX by train for departure back to SFO, and I might even try Nagasaki to KIX, but Nagasaki to NRT is another kettle of fish. Unless you want to try jib71's idea of moving to Fukuoka for your last night, flying from NGS to HND is your best bet. Give yourself plenty of time for the connections and the possibility of road delays between HND and NRT. I would want to be at HND by noon, one at the latest.

If you are flying first or business class, any extra time at NRT is simply more time in whichever executive airport lounge you have access to. If not, extra time at NRT can be spent picking up a few last gifts or souvenirs at the extensive shopping area or a last meal at one of the land-side restaurants. Better to be an hour or two early for that flight home than 15 minutes late.