If you open the player.db file a hex editor, you can edit your points. Go down to offset 2544, then enter the value 286B. This will give you about 27,400 points to start your captain with. It should give you all of the possible sub improvements and leave about 7000pts. to put into your crew.
This can be done before you begin your first mission. All you have to do is create a captain, and then exit the game without choosing a mission. You can use the cheat again after your first mission to get another 27,400 pts. but you will only be able to use about 5000 to max out your sub and crew.