It is sloppy, colloquial English and I don't think it is grammatically correct.
"I have a couple of questions" means "I have two questions" or "I have a very small number of questions."
Adding "just"--"I just have a couple of questions"--adds the idea that it is a small request, a reasonable request.
Adding "is all" at the end intensifies this. It stresses how very little the speaker is asking for.
I THINK it is a shortening of something like this:
"I have a couple of questions, and that is all."
Let me give you a usage example. Imagine somebody asking for a loan.
"Can you lend me a couple of dollars?" (I want two dollars).
"Can you just lend me a couple of dollars?" (I want two dollars, that isn't very much to ask for).
"Can you just lend me a couple of dollars, is all? (I want two dollars, only two little dollars, that's not very much to ask for, I'm not asking for any more than that).