I fear you're trying to re-invent the wheel here. Most of what you're looking for has been done already.
Beery made a Flotilla realism mod some time ago. It fixes the flotilla locations and start dates and is incorporated into both RUB and SHIII Commander, but can also be gotten separately.
Also, RUB is indeed a realism mod, but that doesn't mean it's a lot harder; in fact, some of it's features are actually easier than the stock game. Destroyers and aircraft both behave much more realistically. It also incorporates a version of Rubini's Harbor Life Mod, which adds a lot of ships and planes to friendly ports.
SHIII Commander now lets you switch between different fatigue mods, as well as creating your own.
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