In the Ubisoft/SHIII/Data/Campaigns folder there are three campaign files.
The RND file controls the convoys and random shipping in the game. That one was heavily changed for the RUB and NYGM mods.
The LND file controls all land objects, and is also upgraded if you use either one of those mods.
The SCR file controls all scripted units, that is the ones that appear in the same place every time. RUB has many less ships in the harbor than the Harbor Traffic Mod. Simply download HT but when you open it put the files in a temporary folder. You can name it anything you like but make sure it's not in the SHIII folder. Then look at the different files and take the one labelled SCR and move it to the Campaigns folder in SHIII.
Be sure you are in port and between patrols when you do this. The next time you set sail you will see a wonderful world full of ships and planes.
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