1) Does God have free will?
Yes, he does have a free will. He can choose what he wants to do, fact that he choose good doesn’t mean that he cannot choose bad things to do. (and there are some examples for this, but obviously, I wouldn’t go for them in dispute with atheist)
2) If human evils must be allowed so that we can have free will, then why did God also create natural evils? (i.e., floods, disease, etc)
I see this differently, God created environment and mankind, most of catastrophes and most off disease is just natural consequences of living things, chain of causes and effects. So I don’t think, that every time when is there earthquake, volcano eruption, rain flood, influenza epidemics etc, that this is what God doing for fun. Common. Its just how our world works. Was created that way and it is natural flow of things. And if we look in our solar system, our earth is perfect, perfect, perfect. If it is something wrong, that usually our responsibility. Most of diseases are. Yes we are slowly degenerating, our mankind, gens we are transferring are increase (with every generation more and more) prone to some kind of illness …we are uglier, sicker .. but I don’t think, it is Gods responsibility, it is mostly ours. We messed it up.
3) Why are there over 30,000 Christian denominations all claiming to be the "true Christians"? Which one should I follow and why?
I don’t think, that fact, that there are many denominations are bad. I think opposite. Its good. You can choose. And almost in every denominations there are Christians, true christians who belong to real church (meaning Christ bride, that church without specific name or title, that one, which Jesus created himself).
But remind me, why would atheist want to follow or attend church?
Is it God seeking atheist? If so, I would rather “preach” her gospel. And not small talk about different kind of denomination. But if she would be interested I would briefly clarify for her differences between each churches or denominations … But I mean, isn’t it similar with political parties? Would we be so happy or is it even possible to have just one? What a question. I didn’t really never get this hunt for one happy church… so hmmmm unrealistic.. I don't recall, that I have that kind of naive atheist friends.
4) Is predestination true? If yes, then do we truly have a say in our Salvation? If not, then don't you have blind faith?
I wouldn’t speak about predestination with atheist or seeking one. Ever. Its like red rag to a bull.
(and not just for them) I would avoid this question.
5) Can God create a rock too big for Himself to lift?
Really? That’s childish and philosophical. And it is about exact same as first question, doubting if God is almighty.
6) If religion and Christianity are separate, how did religion come into Christianity?
How are they separate?
7) If Christianity is good, what about those other religions that teach the same moral conduct?
Christianity is not about being good, more about being saved and depend on God. There are so many Christian (including me) witch are not even close to be that characterful, altruist, kind, with good motives and a desire to help better than me in many ways and same time not Christians. I believe that there are many atheist with higher ethics or moral than Christians. Christianity is about relationship with God which is possible thru solely thru Jesus. So Jesus is the center. I don’t know about other religions having that. Or is there some religion who had as a center of their worshiping Jesus?
8) If God is so perfect, then why did he create something so imperfect allowing pain, suffering and daily atrocities?
Same as q 2
9) If God is omnipotent (all-powerful), why did he take six days to create everything? Why not speak everything into existence all at once?
He is creator. He likes creating things, imho. I think, that he likes process too. Why wouldn’t he enjoyed creation process? Look at our earth, so perfect in many ways and for just 6 days?
And also, the God and time is still a mystery. One day could be 1000 days in God, and vice versa. So …
This was fun. I really like your questions

and this (your) thread.also sorry for my en
be blessed