Thinking about your inquiry some more, here are some additional suggestions for you, depending upon how much effort you want to put into it.
The various logbooks maintained by World War II-era merchant ships were the property of the shipping company that operated a given ship. Most shipping companies from that period have gone out of business, with the result that the companies' logbooks have likely been destroyed. However, at the conclusion of a voyage, the "official log" for that voyage was turned over to the Coast Guard. Later the Coast Guard turned over those logs to the U.S. National Archives and Records Administration (NARA), to be stored at the NARA regional facility closest to the port at which the voyage ended. Other sources indicate that CAPE FAIRWEATHER began her 1941 voyage in San Francisco, and there is a good chance the voyage terminated there as well. Another possible termination port would have been Seattle, with Los Angeles a less likely possibility. So it is possible that the ship's official log is to be found in the NARA facilities in San Francisco, Seattle, or Riverside, CA. See http://www.archives.gov/locations/ for additional information on these facilities.
The point is, of course, that the official log of this voyage might shed some light on the period December 4-10, 1941, while the ship was in Manila, and possibly even mention your uncle. The official log, which is less interesting than you may think, dealt primarily with the merchant marine crew, as opposed to the Armed Guard crew, but an event as serious as the death of a member of the Armed Guard crew might have been recorded in the official log. The log might also indicate the exact location of the ship within the harbor, by pier number for example.
NARA also maintains the original copies of Armed Guard officers' reports. These reports were filed by the commanding officer of the Armed Guard unit aboard a ship at the end of the voyage, listing the Armed Guard crew, recording drills, disciplinary actions, damages and repairs, any unusual events, attacks, etc. (Commanding officers were always relatively junior officers: ensigns, lieutenants junior grade (LT.j.g.) or full lieutenants.) Unlike official logs, Armed Guard officers' reports are kept at a major NARA facility in College Park, Maryland, just outside of Washington, DC. The officer's report for the voyage of CAPE FAIRWEATHER would certainly have noted any injuries or deaths among the Armed Guard crew during the voyage. The reports vary greatly in quality and detail, depending upon the diligence of the officer in question. I'm also unsure whether officers' reports were required at this very early point, or became a standard requirement only later. But if an officer's report exists for this voyage, almost certainly there would have been mention of your uncle.
One can do research at NARA facilities in person free of charge, other than photocopying expenses, but obviously that is feasible only if you reside near the facility or can travel to the facility. If located at a distance, you may be able to obtain research assistance from NARA staff in locating, copying and mailing relevant records, for a fee of course.
If you pursue officers' reports at the NARA facility in College Park, you should specifically contact the Modern Military Records Unit at this address:
Modern Military Records Unit
National Archives at College Park
8601 Adelphi Road
College Park, MD 20740-6001
Ron Carlson, Webmaster
Armed Guard / Merchant Marine website