Reading between the lines, I presume the OP has some sort of status that will allow him to use a priority check-in line at NRT (you can only do so many SFO-NRT-FRA flights and not have status). Therefore, I think your 8:28 arrival advice is more than a touch conservative. I wouldn't flirt with the 60 minute mark because I a have a friend who was denied boarding earlier this year for attempting to check in 57 minutes before flight time. However, I think anything north of 70 minutes should be completely ok.

Also, if flying JL or NH all the way, that itin should definitely qualify for a free room in Narita. While Narita is no Tokyo, it is possible to have fun evenings there.