I would also recommend flying SFO - NRT, spend some days in Tokyo, then take the train from Tokyo (Shinkansen) to Kyoto, travel time depending on the train - Nozomi (2 hrs 20 min) Hikari (2 hrs 50 min) or Kodama (3 hrs 50 min), then fly back to SFO from KIX. From Kyoto Station, you can take the Haruka Airport train (about 75 minutes) to KIX. You'll have less travel time overall IME than trying to fly from Tokyo to Kyoto (Haneda to Osaka - Itami), as Kyoto is around an hour's travel time from Itami Airport + the check in times.