I found it... in vicker's mod, the UpgradeClass for the Porpoise is 3, which is the old level, but the Sargo is 1, which is the new level... We'll square that away. There really are no upgrades though at Surabaya. If you're in a Sargo, that is the best they had there, and the only other boats were Pearl or San Francisco based.
To satisfy my curiosity, what are the "FOTRSU Position Keeper Tweak" and "Manual Range TDC" mods?