F1RacerDan: Welcome to the realism club! I'm aware I'm quite new myself to all this, so probably best go with what the old sea dogs say as well, but I'll add my two cents.
For career length, I tend to avoid the 'realistic career length' option as it can retire you early (my latest commander was retired after 80 days at sea). As SailorSteve says, there's not much point in then using the 'unretire' option. A good guide is to go on uboat.net and look at some real commanders (if you can find one who wasn't killed in action) and see how long he did before being promoted to flotilla command or a training position. I've done a quick scout and the longest careers seem to be about 8 patrols, 350 days at sea. So you could voluntarily 'retire' yourself after that.
As for other realism options, I asked this question
here. Some excellent responses there from people pointing out great mods for 100% realism torpedoes - the last link before the end is a FANTASTIC mod for history buffs and realism fans.
And as for crew management, being a bit of a scholar on U-Boat crews (my humility truly knows no bounds here) I wrote
this up about realistic crew management.
Others, feel free to shout me down if you disagree/think I'm mad. But F1, good luck with this endeavour and please let us know how it goes! Feel free to reply with any further questions, i don't mind doing a bit of legwork/research for a fellow realism buff
