On the 777 UA uses on EWR NRT the configuration is 8F, 40J, 113Y+, 108Y. They don't have a Y+ fare per se, but any Y passenger can pay a flat amount to upgrade.
Unlikely that every seat is filled on ever date. More likely 85-95% of Y; 75-85% of Y+; 60-70% of J and 50-60% of F. (These are guesses I have no knowledge of what they actually are)
As a network airline many of UA's customers are connecting onto and off of this flight. As fares are not set sector by sector you need to assume a 20-45% (sometimes more) dilution from prorate costs. (i.e. A passenger travelling from Washington to Singapore could travel IAD-EWR-NRT-SIN. Fares for that journey could be Y/486, J/1890, F/7078 which would have to be prorated over the three sectors. The EWR-NRT flight is about 65% of the total journey giving it Y/316, J/1228, F/4600 from the ticket price before deducting taxes.) ...
Now Children and Infants (and Ship's Crews, Staff, Travel Agents, etc.) get discounts ..
Estimating an airline's total revenue for flight is not easy and is prone to error. In fact the airlines rarely try and track revenue per individual flight. You have likely overstated the potential revenue by a significant amount, and the proportions are likely wrong as well.
And don't forget that this aircraft type will burn something like 8,100kg per hour for a 14 hour flight. Refinery fuel costs are around $429 per metric tonne, airlines probably pay 10% more so the fuel bill alone more than likely eats up all of the Y/Y+ revenue. They you add in the other costs ...
Damn greedy airlines