Yeah, I know from old that designing scripted things is difficult, because the players don't do what you expect them to. As for the sub choice, I had wquite a wide choice and I chose a Tambor class :-).
I don't think many people will like to wait around doing nothing at the start of a mission, it will make them start to look for things to do on their own, which makes it confusing when the messages start coming in.
As for the start, I don't know a great deal about the attack on Pearl Harbour, but I do know that the carrier fleet had left a couple of days before on exercises... how about instead of starting in the harbour, you are part of a group of x submarines assigned to be the carrier fleet's screen on the exercise, when you receive flash traffic warning of an attack and your mission turns from exercise to real and you are sent to scout for the carrier group? You could receive orders directing your fellow subs to scout west and east of Pearl and you to scout north of pearl.
This would mean you started at sea, with the fleet and not in a laggy port (I have a nice machine, but it doesn't like harbours much fps wise).
As I understand it, a fleet of PBYs was sent out on diverging course of 10 degrees each to search for the carrier fleet and it was found by one at almost the limit of its fuel. I'm not expert with the mission editor, but I think you can create a task force and give it waypoints, so they player if he knows where it is can go directly for it. You can also have this task force removed at a certain date and a new task force created at the same spot a minute afterwards, with a contact report. this should, I think, create a contact report at the time you want for the location you want. I'm not sure though - have been so busy, barely had time to try this mission, let alone try something new in the mission editor :-). The contact report would make it crystal clear to the player where he should be heading. It then wouldn't matter if you had already encountered the Japanese fleet, as the PBY report would be sent to all ships anyway.
If you base the exercise southeast of Pearl, you should be fairly safe that there will be no planes.
That's just my thoughts, feel free to ignore them
.