You need to stock some balm (which can be bought in the item shops of a few ports, for example in Marseille). I usually buy 12-15 balms whenever I have the chance. When you get a storm warning, use the balm to calm it.
It's important to keep one of those ports as an ally so you can go buy some balm whenever you need.
Also, buy yourself a cat and you'll never have trouble with rats anymore.
To free yourself from your current situation, you could try sailing back to Europe (Marseille -> balm, though there are a few other ports selling it as well). In order to do so, sail from Bissau after repairing all your ships; when you get a storm warning, go ashore. "Hop" like this until you reach the next port, repair your ships, etc.
Also, it's always a good idea to keep a few older saved games. If something goes horribly wrong, you can always return from a previous point.
Good luck!
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A sickened, sensitive shadow writhing in hands that are not hands, and whirled blindly past ghastly midnights of rotting creation (Nyarlathotep, H.P. Lovecraft)
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