Hi Funkie,
glad you are also a SH3 fan, but with SH5+TWOS I think you have the best sub sim available at this time
For your 3):
Missions and side-missions (secondary missions) are purely time dependant, so when you go out on patrol again they may still be offered to you, but will vanish at some precise date and be replaced by other ones. All this is not immediately visible on the Briefing map when you talk to the BDU officer, but will always appear on your tactical map during patrol. Also keep attention to your logbook and radio messages.
Have fun!
