Well, I was poking through some of the graphics mods and found Pacific Wolf's Pampanito mod, which puts a nice Hi-Res measure 32 paint scheme on a Balao, as well as the Pampanito's hull number. Also his mod ensures that anytime you get a Balao it is always and only the Pampanito. Sure enough, I activated his mod and took a Balao for a single mission; it was the Pampanito. I took a look at his roster file and the only Balao boat in it is the Pampanito, with a few changes to the DOC and DOD entries, so I've edited the Balao.cfg file for the roster and will swap files when I get back to port after my current patrol. Seems you have to deny the game any opportunity to screw up in order to get what you want.
By the way Torpx, if you see this I may still need to edit my career file to make everything work, but I'm still not sure which it is, so please let me know.