If I do try to start a mod, I doubt very much whether I would do any PTO operations at all. I would prefer to focus on the Med and Europe. There are a couple of reason why I think Sh4 is better for this than the first one and it is mainly to do with the way the campaign is set up. The fact that the Sh3 campaign was grid based and SH4 is objective based is the big difference. I've already knocked up brief Med Missions just using what is available in the stock game and it's perfect for the sort of patrols one could realisticaly expect. Plenty of deck gun action too!
Aside from that, there is half a world map full of ports that is virtually unused and there are many possibilities.
For TDC, well. I haven't given any thought to it but I would probably keep it there regardless of whether it is realistic or not. But that is a discussion for the future. I seem to remember someone saying that external tubes ought to be possible.