Been poking around with the menu editor, and other ingame tools.
if I load the game with menu debug info turned on and go to the choose torpedo page I get this
which shows that the extra torps are all ok, and the stern tubes have been added, so I can assume that the upcge file is ok.
The problem is without menu debug turned on, the choose upgrades and choose torpedo lines are greyed out.
start mission and check torpedos on board and we get this
all the extras are here but the stern tubes have been moved to the Bow.
and the crew is still AWOL.
So making a new torps page and crew page will possibly sort the problem out.