I think I fixed it! There was some older information in one of the .csv files.
After discovering that W cycles the forward tubes only, and E cycles the aft tubes only, I dug around the key_commands.csv file and saw that line 55 sets the aft tube cycle to the Y key, which was possibly from an older TMO version, I'm guessing. I changed it to the E key (even though it said "Do not change the ID for this!"). I also noticed that the emergency surface command was still linked to the E key so I just deleted that line, which results in a sh4speech error as it tries to find line 35. Which makes sense because TMO no longer has a key command for emergency surface- it's a button now. So I or better yet, someone smarter than me has to map out the button and parent tab for the blow ballast command.
Anyway, fish control is looking good, although I do wonder why no one else has the issue. I'm thinking now that I downloaded an older version of sh4speech or something, I'll have to look into this.
Edit (again) Maybe this skipper isn't as dumb as his crew thinks. I think my version is the latest. To make the emergency surface command work, delete all line 35 in the voice_commands.csv file, find line 95, and insert this line: "503,Emergency Surface,Blow Ballast,". This will go in preceeding line 504, and will make the BLOW BALLAST!!!! voice command work. Now I have properly working fish, and the ability to get to the top after a signature reckless attack that goes all wrong. :p