the torpedoes is not fixable(I think), just make do with what you're given, or what I do is after firing the first one switch them around by unloading another tube, you'd have to turn the automatic reload off for that. and your torpedo crew will probably mutiny because of long back-breaking labor
as for the days, you can change that to 1 in sh3commander options, unless your boat is damaged, they inevitably fix that, and that takes a set amount of time, but you'll only stay in port the 1 day after that. this is also unfixable (I think)