You wrote and I missed:
> 3. Logistics
I'm not sure if all the vessels in the convoy had the range to make it all the way to Manila non-stop. Of course there was a stopover at Suva to take on fuel and water, but this was only a little over a third of the way (2780 nm from PH) to Manila. We do not know if Pensacola Co[nvoy] was directed to have another stopover - at Port Moresby or Ambon perhaps. Would fuel and water have been available? >
The revised routing instructions, dated 27 Nov 1941, No. 7, reads, "After leaving Point NEGAT, proceed to within signalling distance of PORT MORESBY, NEW GUINEA, where you will be furnished pilots for TORRES STRAIT. Vessels requiring fuel or water at this time may be furnished some at PORT MORESBY."
POINT NEGAT was the last of three specified points the convoy was required to pass through after departing Suva, Fiji, viz., Lat. 12º40'S, Long. 149º00'E. I think you have hit on the reason for the route passing through Torres Strait: by taking a truncated course along the northern shore of New Guinea as you suggested, there was no place to get fuel or water until they were at Tarakan, and the Dutch did not wish this kind of regular contact with the U.S. Navy. As you wrote, it would have been a long voyage from Suva to Manila Bay, and for such reason would appear that proceeding to Port Moresby was the only practical answer.
In my previous I wrote, "One example: the substantial number of American aerial assaults against the IJN's main battle force at Midway before scoring one hit." So not to be ambiguous, of course I mean the First Carrier Striking Force or informally, Kido Butai, which was indeed the primary target for U.S. naval air attacks.