If you don't want to visit Tokyo you could fly UA IAD-SFO-KIX. The SFO-KIX flight is going to use the 787 so it would be a pretty good ride in C, and you could probably get a decent product up front for the transcon as well.
Another option is ITM, which has nonstop service to NRT. It's about a one hour bus ride to Kyoto, not exactly glamorous.