If you're having difficulty figuring out which numbered folder is you, I've found how to get that in my research into the Crew Rotation program I'm working on (which could probably be made into a full-fledged save game editor given enough time, but I'm trying, at least at the beginning, to avoid feature creap so I can get one thing right at a time). Inside each folder is a file called ReplayInfo.rep. Open this file in Notepad, and you'll see a bunch of hexidecimal gibberish (I used python to print out what it actually said, and it's just that. Most likely, the zlib guess is correct, although I'm not quite good enough to sight-read zlib compressed files

). But, in the midst of that gibberish, Success! The format is as follows:
\xnnPlayer\xnn<Name of your save game>\xnn\xnn\xnn....\xnn`Z
(or something roughly approximate to that, I'm at work so I don't have it in front of me at the moment). In this, \xnn stands for a hexadecimal character. It won't show up that way unless you use something that understands hex, and Notepad doesn't. In Notepad, it shows up as spaces and boxes, maybe the occasional character. But "Player" and the name of the save-game shows up flawlessly every time. That way, you can be sure you're editing the correct saved game. FYI: I'm not sure what all that file is used for, the hex within it changed for reasons not immediately obvious to me from save game to save game. CHANGE THIS FILE AT YOUR OWN RISK.
@rhohltjr: Check the file called ActiveUserPlayerUnits.upc in your save game folder (verify you're in the correct game using the above method). On the Archerfish, the After and Forward Gun decks are compartment 7 and 8 respectively. Presumably that will be pretty close to the same on all the boats. So scroll down to Compartment 7 (you can search for "[UserPlayerUnit 1.Compartment 7]") and verify that the "NameDisplayable" value is "Aft Deck Gun Mount". Wherever you find the Aft Deck Gun Mount, the very next compartment is the Fore Deck Gun Mount. Once there, here's a few things to check.
1) Under [UserPlayerUnit 1.Compartment $.WeaponSlot 1] (where $ is the compartment where you don't want a gun), verify that the very last value (IDLinkWeaponLoaded) is set to NULL,NULL. If it's not, set it to that.
2) Make sure that "[UserPlayerUnit 1.Compartment $.CrewMemberSlotAdditionalRepository 1]" is one of the section headers (once more, $ is the compartment where you don't want the gun) and not [UserPlayerUnit 1.Compartment $.CrewMemberSlot 1]
3) Now check that the opposite is true for the compartment where you do want the gun. Check that IDLinkWeaponLoaded is set to something like 4in50calUS, NULL (I'm not sure what the second NULL is for, I haven't gotten that far into it). Also check that the format for the CrewMemberSlots matches those from neighboring compartments. I'd post the format here, but it's WAAAYY long, it's probably easier to save a game with a functional deck gun crew and copy/paste those sections over. Don't forget to change the Compartment number to match the correct compartment in your new game.