The torpedoes are there just none in the tubes.
Load up the tubes and hit re-fit again. I think actually all you have to do is hit the re-fit again.
As to the "end patrol" being greyed out you are NOT at your home port. The game is a little lacking in where it notifies you when your home port is changed. Sometimes it tells you other times it doesent.
Here is a discussion on how to find where your supposed to go..
http://www.subsim.com/radioroom/show...rick+home+port