Need some assistance with some confusing arguments. I'm 18 and recently stopped attending church because I became an atheist last year. My youth pastor has noticed how I've become more questioning and how I've recently distanced myself from church related activities. He gave me a call a few weeks ago and had some questions regarding my own rather potent and critical questions I've brought up in the past. Somewhat incriminating questions like; "What is more likely, that our religion is the one true religion out of say, a thousand other religions, and you only believe in it because it is true. And because of that, if you happened to be born in the Middle East you wouldn't be a Muslim because you can somehow tell it wasn't true? Or is it that you were simply indoctrinated into your faith because of your religious surroundings. And if you were in fact born in the Middle East, you would be saying the exact same thing about Islam?"
And a question about prayer that I've only now been brave enough to ask, "Does wether or not you pray really do anything? I mean the only possible answers are; Yes, No, and Wait. And 'wait' turns into either yes or no eventually anyways. Plus, if the answer is 'yes', that means 'God is so good' if the answer happens to be no, it's 'well God knows best anyways' Or is swiftly swept under the rug. Bottom line being that something would've happened either way. Attributing god(s) to it is as meaningless as saying Unicorn did it, isn't it?"
Note that these questions were not nearly as concise when I said them compared to how I just wrote them. There was a lot of stammering like a moron I can assure you. Anyways, now that you understand the context of questions I was asking, I would like some help with the arguments and counterarguments my youth pastor posed to me:

#1.)
"The problem of good"
This argument seems like some kind of mirror image of "the problem of evil". I don't know everything about the evil problem, I'm probably wrong, but I think I understand what it boils down to. I think "the problem of evil" is just a simple rebranding of "if god is good, why is there evil?". I'm not very well versed in atheist arguments, but I'm assuming by the same logic, "the problem of good" is the theists way of flipping "if god is good, why is there evil?" on its head changing it to "if there is no god, why is there good?" So my youth pastors position is that there is proof for god because most people have the need to help other people when in need. But because people are god's special creation, and that if it weren't for his grace and the word of the bible, everyone would just be savages. I pointed out that many animals have altruistic behaviors and it's not exclusive to humans, we are animals just like they are. And that there are many people who have never read the bible who do good things. This must've not been a good point of me to make because he insisted I was incorrect (he wouldn't specify on which part) he continued on to say: "Well the naturalists are still left with the problem of good. If we are just a bunch of atoms bouncing around, where does want to do good come from without the presence of a god?"
Apparently I was not smart enough to take the argument any farther. This is where I was stumped unfortunately. I thought I might ask then "where does god's sense of good come from then?" But I thought that would just lead to some dead ended circular response like "God is the definition of good." Or "doesn't apply. God isn't made of atoms, stupid."
Can someone explain how to respond to the problem the problem of good the naturalists have? Or correct me if my line of reasoning is dead wrong?

Question #2)
"We can know the bible is true because of the many prophesies the bible has verified."
This line of argument is a bit specified for me to keep up with honestly. My youth pastor says that the events of the bible are confirmed by history like ancient records in Egypt and such. And that the bible is like "double true" because it predicts things even today. I wish I could remember what he said that the bible predicts currently. But they were too vague and general for me to remember. I'm skeptical, to say the least, that history in fact confirms the bible. But I don't know of any examples in history that would refute that claim. Besides the fact that the story in Genesis is just a myth. But like 10 plagues, the Exodus of the Israelites or crossing the Red Sea. I mean there must a metric crap ton of evidence for that.
What claims don't match up? What about the prophecies? Have any of them really been confirmed?

I'm rather new to this site, looking to make some new friends it at all possible.
Anyways. Hope my long winded questions made some sense. Thanks so much!