Could the flaws in the Torpedoes be fixed out in the field?
Actually, IOTL the firing pins were field-modified by subtenders and forward base teams quite successfully. Disable the magnetic exploder (again, any tender or base could and sometime did do this), set to run at minimum depth (depth was selected just prior to firing), and with a field-mod pin you'll get a decent hit & detonation rate.
The problem is how someone finds out that the torpedoes (actually, mostly the detonators) had problems. IOTL there was NEVER a live-fire test. Yes, you read that right. The Navy contracted a single manufacturer to build just about the most expensive piece of ammunition they bought but never did a live-fire test.
The detonators were considered so awesomely powerful and secret that they were kept at shore stations, not issued to ships.
The flaws were so many (ran too deep, magnetic exploder didn't work, contact exploder unreliable...) that it took months even after the stateside ordnance REMFs admitted there was a problem (roughly a
year after the sub skippers had concluded there were fundamental design flaws) to find and fix them all.
Back to the OP, have Mac break his neck on December 1st. Command will pass to MG Wainwright, who was at least competent and fairly aggressive. He's only got a week to put his house in order, but that's better than nothing. He'll certainly grant Brereton's
first request to bomb Formosa (IOTL Mac ignored even his
third request). The FEAF won't be caught on the ground, and they'll do at least a little damage. Perhaps even a lot - the B-17 was a plane the Japanese didn't have a good counter for in the first days of the war. Wainwright can't possibly work with Adm Hart any more poorly than Mac did, so some coordinated Army-Navy action is possible.
Is it enough to hold Manila for six months? I don't know, but it would certainly prolong the PI campaign.