sangho - I would be aggravated too, if I was 1K and had 6 GPUs to use, and my international upgrades on W fares constantly failed to clear. I cannot speak to the EWR-NRT route. But I often fly SFO-NRT. There are 2 B747 flights a day. On a trip I'm making shortly, there was R9 availability at booking both flights, both directions. This remains the case. Although I'm flying on a Wednesday, I see R availability weekend days too.
Think positive. EWR-SFO-NRT is more miles!