I can't answer the question of Jewish idioms or whether it was normal to say 3 days, 3 nights and mean something else but I can say this:
I'm not referring to the use of symbols when I say this but if the bible was written in ways that make what it says different from what it means then we shouldn't base our belief system on it. Otherwise, at that point, you can just do what JWs and other religions do, and make it up as you see fit and start any number of cults based on your newest understanding.
IMHO, if god wanted to tell us something, he would do it. He wouldn't make it so obfuscated so as to hide the message in shrouds of discrepancies, leaving people to figure it out on their own. Some may counter: "yeah but he can give you holy spirit to understand.." to which I say " then we don't need the written word at all, he can just make us understand and the holy spirit can teach us all things as Jesus said"
Too bad it's all nonsense, as the many serious discrepancies (like the one cited in the OP) make super-abundantly clear.