I am still reading your interesting post #306!
A few questions/comments:
You state:
"CT water scavenge jet pumps get motive flow from the CT boost pumps, so only operated when CT boost pumps do"
Are you 100% sure that is the case? Info from the AMM?
I agree with the info re pitch attitudes given by Chris Scott.
You suggest that the crew might have left the CTR pumps running for the whole flight. I do not think they did!
I have not flown the 777, but the 767 with a much similar fuel system.
If you do not switch the pumps to OFF acc. SOP, you will get an EICAS message + caution lights in the pump push buttons on the overhead panel.
It is VERY unlikely that any crew would sit for hours without taking action.
BRGDS