Download/install
WinMerge
Make a copy of the folder where your modmod is installed
Open WinMerge, and select the Open option in WinMerge.
Check the box that says "Include Subfolders"
Browse and select the base FfH2 folder next to "Left," and the Copy of your modmod next to "Right."
Press "OK" and wait until all the files in these folders are compared.
Go to the "View" menu and make it so that only "Show Identical Items" and "Show Binary Files" are checked.
Delete every file in the copy of your modmod that is identical to the equivalent file in base FfH2.
Press Refresh (F5)
Go to the "View" menu and make it so that only "Show Different Items" is selected.
Double click on each file that shows up in order to open a tab comparing of these different files.
Use the "Next Difference" and the "Copy Right" to any More Naval AI specific code to your modmod, being careful to keep your own modmod's changes in place too. You my have to make some changes as you go.
Save the changes to the copy of your modmod.
You'll probably want to open each of the python files you change in another editor such as IDLE or PyScripter in order to use the debug feature. Merging Python files in Winmerge often introduces a couple minor errors, usually related to improper indentation.
At this point the copy of your modmod folder is probably is such a condition that you could just release it and have other people install it over where More Naval AI is installed. I expect people would prefer it if you made it independent on MNAI and only required FfH2 installed. They would also prefer if you try to play the game to make sure it works first.
Make a Copy of the More Naval AI folder, and drag the contents of the copy of your modmod's folder into it. Select yes to overwriting all of the files with the same name.
That should leave that folder as a working version of your modmod including More Naval AI. Open that modmod and playtest it. Make sure that C:\Users\{insert your user name]\Documents\My Games\Beyond the Sword\CivilizationIV.ini has been edited to enable logging, and use the contents of C:\Users\Magister\Documents\My Games\Beyond the Sword\Logs to track down any errors.
Open Winmerge, go to the "View" menu and make it so that only "Show Identical Items" and "Show Binary Files" are checked, and start a comparison between the base FfH2 folder and the Paradeignma + More Naval AI folder.
Delete any files from the Paradeignma + More Naval AI folder that are still unchanged from base FfH2.
The Paradeignma + More Naval AI folder is probably ready to be released, but you should test it first too. Copy its contents into a copy of base FfH2 and playtest it.
Compress Paradeignma + More Naval AI or use a program like
Inno Setup Compiler to make an exe installer.
Release your new modmod.