Assalaamu alaykum. I have been pondering how to logically refute atheists, and I have been going over an introduction into it. I fear that because of how I introduce my speech, perhaps it is Shirk (polytheism) or Kufr (disbelief), even though I do not intend it so. This is the start of that refutation:
The very first question we must ask is if there is a God or not. If there is no God, then literally nothing we do matters, nor anything we discuss. If there IS a God, then we ask if there is an afterlife or not. If there is no afterlife, then it does not matter if God exists or not. If there IS an afterlife, then we must ask if it is both heaven or hell, or just heaven, or just hell. If it is just heaven or just hell, it does not matter what we do as we will all go there anyway, but if there IS both places, then there must be a criteria for entering into each. If there is a criteria but we do not know what it is, then again it does not matter what we do, and if the criteria is just doing what is right, everyone in the history of mankind has only done what they thought was right and that includes evil people as well. If God has a criteria, the only trust-worthy source is from God Himself, and how does God inform us of the criteria? He sends Messengers. How do we differentiate true Messengers from false ones? The Messengers will come with miracles that only God could have given them. The greatest of these miracles (and may Allaah forgive me if all the miracles are equal in greatness, I say what I do out of ignorance but without intent to say what is impermissible) is the enduring one, and today that would be the Quran, because it gives us access to the miracle every day, and it is a miracle of logic, of the mind.
Please tell me if this introduction is Shirk/Kufr, especially as at the start I begin my explanation with questioning whether or not God exists. I question God's existence at the start of the introduction because the atheist starts from the belief that God does not exist, so I refute from there.

All perfect praise be to Allah, The Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad is His slave and Messenger.

First of all, we thank you for being keen on inviting people to Allah Almighty and guiding them to the straight path. We ask Allah to bring good to the people at your hands and make you a reason for their guidance so that you get a great reward, as the person who guides people to do good gets the same reward as those who do those good deeds.

Abu Hurayrah, may Allah be pleased with him, narrated that the Prophet said, “Whoever calls to guidance receives a reward similar to the reward of whoever follows him without that diminishing anything from their rewards.” [Muslim]

The questions that you asked do not involve any kind of Kufr or Shirk as you asked true questions as an introduction to lead them to correct results. This approach exists in the Quran, such as the saying of Allah (which means): {Or were they created by nothing, or were they the creators [of themselves]? Or did they create the heavens and the earth? Rather, they are not certain.} [Quran 52:35-36]

There is much evidence in the Quran and Sunnah, both textual and logical, to prove the existence of Allah Almighty, the truthfulness of the Prophethood of Muhammad and the proof of resurrection after death. In this regard, please refer to fatwas 81529 and ">22055.

Finally, we would like to point out the following matters:

1- There is nothing wrong in describing the Quran as the greatest miracle, because miracles vary in their degree. The Quran is one of the greatest miracles because it is a permanent miracle that will remain throughout the ages. It is for this reason that Prophet Muhammad to whom this Quran was revealed, is among the Prophets with the most followers.

2- A Muslim who debates with the atheists and the people of falsehood must have firm knowledge of the religion in order to refute their misconceptions. Please, refer to fatwa 340435.

3- It is important to avoid Waswaas (obsessive doubts) about committing Kufr/Shirk because doubts in this regard lead to bad consequences. The scholars have written chapters in their books about apostasy and clarified what takes a person out of the fold of Islam. There are criteria in this regards, which we have highlighted in fatwas 8106 and 87963.

Allah knows best.