Is the Qur’an Completely Clear or Not?

”Qur’an Contradiction "

The Qur’an emphatically states that it is a clear scripture,   

Alif Lam Ra. A Book whose verses are set clear, and then distinguished, from One All-wise, All-aware: S. 11:1

A book that fully and clearly explains everything,

… Shall I seek a judge other than Allah while it is He Who has sent down unto you the Book (The Qur'an), explained in detail… S. 6:114 Hilali-Khan

… And We have sent down on thee the Book making clear everything, and as a guidance and a mercy, and as good tidings to those who surrender. S. 16:89 Arberry

A Book whereof the Verses are explained in detail; A Qur'an in Arabic for people who know S. 41:3 Hilali-Khan

The implication of the aforementioned texts is that all of the verses of the Qur’an are clear and that the Muslim scripture doesn’t contain any passages that are obscure or difficult to grasp.

Yet this is contradicted by the following verse that says that there are passages which are not entirely clear, whose meanings are known only by Allah:

It is He Who has sent down to you (Muhammad) the Book (this Qur'an). In it are Verses that are entirely clear, they are the foundations of the Book [and those are the Verses of Al-Ahkam (commandments, etc.), Al-Fara'id (obligatory duties) and Al-Hudud (legal laws for the punishment of thieves, adulterers, etc.)]; and others NOT entirely clear. So as for those in whose hearts there is a deviation (from the truth) they follow that which is not entirely clear thereof, seeking Al-Fitnah (polytheism and trials, etc.), and seeking for its hidden meanings, but none knows its hidden meanings save Allah. And those who are firmly grounded in knowledge say: "We believe in it; the whole of it (clear and unclear Verses) are from our Lord." And none receive admonition except men of understanding. (Tafsir At-Tabari). S. 3:7 Hilali-Khan

So now which is it? What are Muslims supposed to believe concerning the nature of the Qur’an? Is the entire Qur’an clear and fully explained, or are there parts of it which are unclear and whose interpretation only Allah knows?

Finally, how does a Muslim know for certain which verses are clear and which are obscure when the Qur’an nowhere delineates the two?

IHS