I'd prefer the direct Portland-Narita flight. I had the necessary 180,000 Alaska Airlines miles needed to buy two business-class tickets on Northwest. I called on the very first day that you could actually buy a ticket for our travel dates (330 days before the return date). But the Alaska agent informed me that Northwest only allocates one business-class seat per flight on that PDX-NRT route. Therefore, we get the PDX-SEA-HNL-NRT routing instead in order to get the more comfortable seats. In the end, being able to travel in comfort is more important than getting there quickly. Lisa hates flying in commercial airplanes enough as it is. She'd go completely bonkers if she didn't have a pair of business-class seats with me (2-2-2 seating; we're on the left side, about mid-way through the class cabin on every applicable leg).
And no, we're not doing a stopover in Hawaii, just the three hour layover at Honolulu airport. Going back to Hawaii is somewhat more likely than making another trip to Japan, so we're trying to maximize the use of my vacation time in Japan.