Re: He said it is/was going to rain.
I would backshift to "was" in that case, but if he just said it a moment ago and I simply couldn't hear him, then "is" is okay.
Him: It's going to rain
Me: Sorry, I couldn't hear that.
Him: It's going to rain.
Me, to you: Could you hear him?
You: Yes. He said it's going to rain.
Me: Thank you. You don't have to shout.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.