After reading some of the claims listed on the site you linked to, I can conclude that there is an element of misinformation behind the content. And because there is so much of it, it would be unfair to expect me to sift through the material and provide a rebuttal for each claim. So I will direct you to a book which, if you sincerely desire the truth, should answer your question: http://islamicbookstore.com/b7626.html
If the Qur'an has never been altered, what about all the claims that it has listed here: http://www.answering-islam.org/Quran/Text/
The Muslim Perspective
Is a deistic god possible?
Can you explain Naskh and izala within the Qur'an? What do these terms mean and do you accept their practice? Why or why not?
Why does God require an argument to defend it, unlike something obvious like gravity for example?
Answers: Muslim, Christian
Do you believe the laws of logic are invariant and universal? If so, how can you justify this belief? If not, can you provide an example?
Mr. McCabe, you obviously don't read your own Bible. On the first page alone (Genesis) in the Arabic Bibles around the world the word Allah is there 17 times. YHWH was only given in Exodus, there aren't any vowels, so why did you say Yahweh?
Muslim Islam vs. Islamism: The Dilemma of the Muslim World Asghar Ali Engineer Muslim A Living Faith: My Quest for Peace, Harmony and Social Change Asghar Ali Engineer Muslim Islam in Contemporary World Asghar Ali Engineer Muslim On Developing Theology of Peace in Islam Asghar Ali Engineer Muslim Islam: Misgivings and History Asghar Ali Engineer Muslim The Prophet of Non-Violence: Spirit of Peace, Compassion & Universality in Islam Asghar Ali Engineer Muslim Islam: Religion, History, and Civilization Seyyed Hossein Nasr Muslim Welcome to Islam: A Step-by-Step Guide for New Muslims Mustafa Umar