It's really too bad that there is this common image of religious peopleas simply swallowing what someone else has told them. I don't know manysuch folks myself, though I am sure they do exist. And if the people at your son's church are telling him to stop asking questions, that's even worse: Questioning is not opposed to faith but an integral part of it, and a faith based upon just not questioning is not a faith that will survive very long. Maybe you and your wife should find a different church if this one is not serving your son well.
But whatever you decide on that score, there is no reason you can't engage your son's questions. The three you report are very different. (And, not to torpedo your pride, not uncommon: Children are amazing.) The first concerns the second creation story in Genesis. (If you don't know, there are two such stories, drawn from two different traditions.) Assuming your wife isn't committed to literalism here, then the first thing to tell your son is that this is a story, and then you can discuss what that aspect of the story might mean. I'd strongly recommend Marc Gellman's Does God Have a Big Toe? first for you and then for your son as an example of what it means to engage these stories. (You don't have to be a Christian, or a Jew, to do so. We can talk intelligently, after all, about Shakespeare.) The other two questions are much more philosophical. I'm not sure what the second question is getting at. Perhaps your son is struggling with the idea that there might be something that is non-physical. If so, then that's a nice question to discuss. (Where is love? Where are numbers?) The third is indeed a classic question. Did God make God? If not, what does that mean? And, again, one can certainly wonder about what precisely it is supposed to mean that God "made" man. That's part of the creation story, and it's not a part one has to take literally any more than one takes any other part of the story literally.