I don't think Flurry and Rapid Shot stack. They're essentially the same effect (trade a -2 penalty for one extra attack), except that the monk version works on a different set of weapons.
TWF definitely does not stack with Flurry, even if you could use it with ranged weapons, which you can't.
TWF definitely does not stack with Flurry, even if you could use it with ranged weapons, which you can't.