I recently got the game Silent Hunter 4, and while I have some familiarity with land based military during that period I don't know a lot about naval warfare.
The game manual says that ideally torpedoes should explode right underneath the target's keel - as opposed to a contact triggered detonation on the target's hull. Based on that description, it sounds like ideally the torpedo should not hit the hull, but be right underneath the ship when exploding. Why is underneath the keel the ideal position? And given the magnetic detonator's unreliability, did most US submarine captains try for the magnetic detonation under the keel or fallback to contact detonation against the side?
Under what situations would a US sub opt to use the deck gun instead of torpedoes?
If using the deck gun against a steel-hulled ship like a troop transport or a merchantman, would they use AP or HE rounds - or what determinants would favor one over the other? I'm assuming that HE would be preferred against wooden hulled ships.
Which planes would the Japanese use to try and sink US submarines - did they tend to use single engine fighters, double engine bombers or dedicated flying boats like the PBY Catalina?
When traveling long distances, such as to get from the base to its patrol point, would the sub generally travel most of the distance completely surfaced, partially surfaced (i.e. only the conning tower visible), or something else? Would a submarine only submerge when it made contact with an enemy vessel or would it submerge as soon as it reached the enemy zone of control?
After launching a torpedo attack on an escorted convoy, would the sub stay and observe to confirm the kills, or would it normally begin exfiltration as soon as it fired all of its torpedoes?
Aiming torpedoes was a multi-person job. You would have several crewmembers plotting the target and establishing it's course/speed/zig-zag pattern, as a prerequisite to firing. The captain or executive officer would be behind the periscope to take brief observations heading into the target. Other crewmembers would maintain the analogue aiming computer and it's prediction system.
The US started the war with a doctrine of using the new magnetic detonators. Official doctrine was to set the torpedo to pass just under the ship, when the detonator would then trigger. Detonating under the vessel was absolutely more effective, as it would cause a significant negative pressure when the initial shockwave collapsed, leaving the target's keel unsupported and causing it to snap. Striking from the side, on the other hand, primarily used flooding. Soon after war operations began, captains began reporting problems with the torpedoes, claiming that they could see the wakes passing straight under their targets with no detonations. Some captains began switching to the impact detonators against official orders, for more reliability, but even then many claimed that the torpedoes were not working correctly. It wasn't until July 1943 that official tests revealed that the torpedoes frequently ran deeper than set, that the magnetic detonator had problems, and that even when the impact trigger struck it was often too fragile and did not detonate the torpedo. It wasn't until late 1943 when American torpedoes had some level of reliability. The Germans had a similar problem with their torpedoes early in the war, during 1939-1940, but were much faster in solving their issues. The reasons the Americans took so long was because of a number of factors, such as a shortage of torpedoes that limited testing, as well as the fact that one of the top leaders of the American submarine forces, Ralph Christie, had been in charge of developing the magnetic detonator and had faith in its abilities.
Deck gun usually only used against small boats and emergency self-defense, rarely against any armed opponent. Submarines are fragile things and have big problems with getting hit by bullets/shells. Late in the war, as American submarines could afford to be more adventurous, the use of the deck gun increased, even shelling Japanese shore targets.
I don't believe American submarines were issued with different shell types. German submarines were not, and had traditional HE rounds. Anything a submarine would be shooting at with a deck gun was very unlikely to be armored.
Japanese ASW patrols were varied depending on theater/time. Carrier groups would use battleship/cruiser launched floatplanes like the F1M, or spare carrier based attack aircraft like the B5N, to patrol around the carrier force at sea. The IJN operated a large contingent of heavy flying boats, like the H6K for long range reconnaissance and patrols. Other patrols could also be launched by bomber aicraft like the G4M. The last American vessel sunk during the war, the USS Bullhead, was sunk by an obsolete Japanese army Ki-51 attack aircraft.
Depends. Original American submarine doctrine was extremely conservative, stating that the submarine should be submerged throughout the day and then surface at night to get air/recharge batteries. This of course changed as the war developed, with many submarine captains preferring to cover large areas on the surface during the daytime, crash-diving as needed if they spotted aircraft/patrols. Submarines transiting between Hawaii and Midway en route to patrols did not need to dive apart from daily trim checks because of the low risk. However, operating just off the Japanese home islands, many preferred to stay submerged at day. It was a trade-off between area covered and safety. For attacks, the same conservative approach was present in the beginning, with captains being recommended to conduct submerged, sonar only attacks. This was of course inaccurate. If the submarine needed to end-around and get in front of the target, it would do so at flank speed on the surface and far enough away from the target to be undetected. Later when radar became commonplace, it became popular to approach with only the radar mast exposed, before diving to periscope depth for the final approach. Night attacks were frequently conducted entirely on the surface.
Again, depends. If the submarine wanted to make another attack, it would try to surface and flank around for another approach. If against a lone ship, stick around until it sinks or finish it off with another torpedo.
EDIT: Forgot good sources. Thunder Below by Eugene Fluckey is a great memoir for these sorts of operational details, and also has lots about the torpedo chrisis. Silent Victory by Clay Blair is a good general (but still detailed) overview. Gallantin and O'Kane are other captains with good memoirs, blanking on the title.