Questions 1,2 are the same.
Question 3: if you want to reffer to a specific kind/ species of cod, then it would be, "That is my favourite kind of cod."
Question 4: "Cod is my favourite fish" (same as 1,2)
Question 5: "fish" is the same in singular and plural form so you don't have to turn "cod" into a plural too, if you already have "are" (which reffers to (many) "fish"). Rather say it as you have in question 1,2.
Question 6: same as in question 1,2. If you want to make "cod" a plural make "fish" plural ("cod fish are water creatures" (or something :D I don't know anything about cod!) or like you did in question 10)
Question 7: rather say it as you did in brackets ("I like those cod species more than other cod species")
Question 8: same situation as in question 6.
Question 9: yep, same as in question 1,2. You can also specify that you prefer them as pets.
Question 10: perfect!!
Question 11,12: same situation as in 3...
Good luck!! ;)