1. The Quran states it is a sure and certain guide that explains all within it.
2. So you should have no problem showing where the verses are that explain the 3 letters that appear at the begining of some of the chapters of the Quran.
3. From a historical perspective:
If the Quran indeed is a clear and sure guide that explains all within it:
Why did the followers of Muhammad break into two groups upon his death?
Each group differing in how to understand the Quran. Even those who knew Muhammad differed in their opinions. Proving even Muhammad himself was no clear and sure guide.
4. Early in Islamic history there occured serious differences on the topic of man's free will and predestination by Allah.
The two sides both quoted from the Quran to prove their position.
That would not be possible if the Quran is a clear and sure guide that explains all within it.

1) The Quran is indeed a book of guidance that means it show people the way to salvation and how to please Allah, that does not necessary means that the Quran has to spell letter by letter and word by word to go about things in that context. As for the letters he refers too, this is in fact part of the miraculous nature of the Quran to the Arabs then and the Arabs of today to bring a Quran similar to this Quran since the Quran is made of these letters why can’t you produce something similar to it if you claim that it’s Muhammad who made it up. Secondly we are told in the interpretation of the Quran by Ahlulbait that if these letters put together they form the great name of Allah that if you use it to engine Allah by it your prayers will be answered.

2. As in reply to 1.
3. The Quran endorses the concept of free will, thus Allah wants people to follow the guidance by choice not by force if some people wish to divert from the truth that is their choice it’s not an indication that the Quran has a problem rather it’s the people who wish not to follow it. Why are the Christians divided into more that 10 to 30 sects don’t they have the sand bible that each sect claim to be following?
4. The Quran was left for us as a guide by The prophet but the prophet also said to be able to understand it you must follow my family those who have disputed about predestination and free well are the ones who refused to abide by the will left behind by the prophet to follow his household .