[aanker]

From my notes, fast and dirty because I'm in a hurry:

In C:\Documents and Settings\yourname\My Documents\SH4\data\cfg\SaveGames\ find the save game you wish to edit and open "ActiveUserPlayerUnits.upc" with Notepad.

[UserPlayerUnit 1]
ID=Gato
NameDisplayable=Gato
UnitName=USS Drum <<<--- re-name the sub here, USS Peto (SS-265) or whatever.
UpgradeClass=

There are four upc files you need to edit for an existing career:

Open them with Notepad.

Find your boats name, then change it to what you want.

Careertrack.upc

Another is ActiveUserPlayerUnits.upc

Inside a folder named UPCInitial you'll find files with the same names, change these too.
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In Data\UPCData\ look in UPCCampaignData, then open Flotillas.upc to study how that is set up fo your "fleets".