[Didymos Thomas]

And this could be why they so stubbornly cling to their Qu'ran

What do you mean 'stubbornly cling'? If you mean Islamic fundamentalism, this is the result of radicals taking everything in the book literally - which misses the point of the book.

if you look at it closely, alongside of the Torah, Gospels, and Epistles, which it claims to be the fufillment of, there's so many true contradictions; Contradictions / Difficulties in the Qur'an.

The Torah, Gospels and Epistles are also full of contradictions.

Looking through this link you provide, it seems like the author was more interested in finding apparent contradictions in the book rather than understanding the book. Checking the main site, I'm appalled by the blatant misrepresentation of Islam promoted by the site.

Faith needs to be tempered by reason, and reason needs to go as far as possible before we play the "faith" card; God is a god of logic, order, and reason; would He expect His followers to be the opposite?

Depends on which conception of God you appeal to. The notion of God has changed over time. We see contradictory notions of God in the Bible.