Pirates of the Inner Sea has the rules for that in the equipment section. It doesn't mention any downsides to the eye patch but for the others...
Hook hands cannot be used with two-handed weapons, and a character with two of them can't wield weapons at all. If they don't have a wrist though, then they have to have a prosthesis. All you can do with a prosthetic arm is slap a shield on it, so keep your wrists if you can.
Peg legs reduce speed by 5' and give a -4 to swim, acrobatics, and climb checks (half damage from caltrops). Two peg legs can indeed be worn, reducing your speed to half and imposing a -10 to swim, acrobatics, and climb checks (no damage from caltrops!). Prosthetic legs impose a half speed penalty, but no other beyond not being able to have two of them. So protect your knees if you want a peg leg.
According to my search, the Skulls and Shackles Player's Guide should also have a table for scars and amputations. On my copy, it is page four. That says that the penalty for losing an eye is a -4 to perception.
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Rather than using the massive damage rule as the trigger for what causes an injury, I'm planning to make it so if someone gets a natural 20, and then confirms the critical with another natural 20, they have to roll on the table. Should be rare enough to be exciting, while also being possible to happen at low levels.