1. I'd say stick with the Baltic mission and finish it. I don't believe you can get to Scapa Flow and back in time. I went into Danzig harbor and nailed a few escorts before we took it over. After that I didn't see any more Brit shipping so I went up by Copenhagen and sank a few neutral ships. At least that completed that mission. Then transfered was to Wilhelmshaven. Then pick the 'Break the Fortress' mission before you do the Coastal Waters mission. If you don't it will disappear if you go with the Coastal Waters.. at least it did for me, so I went back to the 'in base save' after the Baltic mission.
2. 14 days, unless you change time in base to something less. TDW has a thread on how to do that.
3. You can refit at any German base without docking, just get close so the anchor docking icon flashes. Also know you can't select your torpedo loadout unless you are dock at your home base.
Good luck and sink em all.
