Pigboats can be played either as officers on a single sub, or in troupe mode, with each player playing a skipper of a sub and as an officer on each of the other subs. Turmoil in Truk is based on the first, single sub variant.
This mission takes place in September 1942. That means torpedoes that don't work most of the time - but no one believes you when you tell them this, superiors thinking this is just like the peacetime Navy and the goal is to get ahead - or who hadn't yet shown their complete incompetence, supply snafus, getting our butts handed to us by the Japanese Navy again and again, and trying to figure out exactly how and where our subs might be best used.
As for the mission:
1: The primary mission is to patrol around Truk and sink ships. The recon mission is a secondary mission, tacked on by the squadron commander. If the PCs just do this patrol bit and sink something, their mission will be a success no matter what happens with the recon mission, and the PCs should really enjoy it.
2: It is driven by the sub squadron commander because it would be a feather in his cap on his way to becoming admiral. He is a dick.
3. It is assumed the recon will be performed by an inflatable boat, not by the sub. This is not to say the sub cannot get in - PCs can be wildly inventive - but it would be extremely difficult for one reason or another. If the sub is detected in Truk lagoon, it will almost certainly die. The water is too shallow and too clear to hide in. Even going in with an inflatable is extremely dangerous.
4. The PCs should know beforehand that this is an idiotic 'suicide mission'. They may just say they tried and failed. They may indeed try and fail. They may try and succeed. It's up to them.
5: Should the recon mission be accomplished, however, we are talking Medal of Honor for the skipper, and Navy Crosses for others. Major league Notice.
6: I never give a rat's ass what "actually happened" in the war after the game start date. Once a PC sets foot in the world, it's immediately alt-history from that point forward. :D