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I am curious about how Islam regards those who wish to believe in it and consider themselves Muslims yet cannot spiritually and intellectually come to terms with accepting something just because it tells them

The revelation of the Book (this Qur'an) in which there is no doubt, is from the Lord of all that exists) (2:1-2).

Personally, I am not inclined to accept anything that starts off by claiming uncorroborated authenticity without much proof. Are not taking things at face value, scrutiny, and seeking reasoning in pursuit of strengthening faith vs. just accepting it as unverifiable dogma something that is allowed in Islam?

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    Definitely, yes. God gave you intelligence so that you can think, by helping you observe things around you and conclude, there is something which created everything. And as for the authenticity of Qur'an, see also: this and this. – servant-of-Wiser Aug 25 '15 at 3:21
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    A bit vague when you say "does Islam allow," do you mean whether the Muslims have appreciated that kind of doubt, whether there have been precedents of doubt from history or scriptural references to such allowance? – user549 Aug 25 '15 at 11:08
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From the Scriptures

Quran narrates for us the story of Prohpet Abaraham (puh) who despite being a prophet wanted to set his inquisitive intellect at peace.

Call to mind the other event also, when Abraham said, "My Lord, show me how Thou bringest the dead back to life?" He said "Have you no faith in this?" Abraham humbly replied, "I do believe but I ask this to reassure my heart." ... (2:260)

Another example is quoted of, who is believed to be Prophet Ezra (puh):

Or take the case of the one who passed by a township that had fallen down upon its roofs. He exclaimed, "How shall Allah bring back to life this township that has become dead?" At this Allah caused him to die and he lay dead for a hundred years ... (2:259)

We may not say that prophets had doubt - in the general sense of the word "doubt", but rather the quest to attain greater surety of faith as corroborated by Quran:

And thus We showed Abraham the kingdom of the heavens and the earth, so that he might become one of those who have sure faith.. (6:75)

The point to be taken from these verses is that faith does not come as white or black, but rather as a grayscale of certainty.

Muslim Thought

There is probably no greater exponent of doubt as the first step to certainty than Al-Ghazali, one of the most influential figures of medieval Islam. In his autobiographical work al-Munqidh min al-Dalal (Deliverance from Error), he narrates how be became a skeptic until he could no longer rely upon neither his senses nor reason for curing his "disease" of doubt and attaining "certain knowledge." There is a school of thought, including orientalists, who trace origins of Descartes' doubt to be in Ghazali's Munqidh.

Let me quote directly from Munqidh. I strongly urge you to read the whole treatise.

Certain knowledge is that in which the thing known reveals itself without leaving any room for doubt or any possibility of error or illusion, nor can the heart allow such a possibility. One must be protected from error, and should be so bound to certainty that any attempt, for example, to transform a stone into gold or a stick into a serpent would not raise doubts or engender contrary probabilities. I know very well that ten is more than three. If anyone tries to dissuade me by saying, No, three is more than ten, and wants to prove it by changing in front of me this stick into a serpent, even if I saw him changing it, still this fact would engender no doubt about my knowledge. Certainly, I would be astonished at such a power, but I would not doubt my knowledge.

Thus I came to know that whatever is known without this kind of certainty is doubtful knowledge, not reliable and safe, that all knowledge subject to error is not sure and certain.

Have I answered your question directly? I'm not sure that I have, but I have endeavored to show that your condition in not unprecedented in the history of faithful.

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Can you say you have accepted something but then once you go through it you say... "no I am accepting this part or that part" No... You have then accepted only those parts... not the whole. The Quran is saying... ONCE you have accepted it as THE BOOK, then if you disapprove a part of it, then you have disapproved the whole book!
Your question applies to both before accepting and after accepting the book.

If its before acceptance: then you have still not accepted it and need to go through it. Why is OK by Quran. If its after acceptance: and then you just don't want to approve 'a' part of Quran then that is identical to you of not accepting it as a whole!

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So if you (O Muhammad SAW) are in doubt concerning that which We have revealed unto you, then ask those who are reading the Book before you. Verily, the truth has come to you from your Lord. So be not of those who doubt (it).10:94

Allah (swt) always says to use your reason when you are in doubt, use previous revelations, use what you see around you to reaffirm your belief.

As for the verse you provided, you're clearly reading it out of context:

2:2 This is the Book about which there is no doubt, a guidance for those conscious of Allah -

It doesn't say there is no doubt about the book, rather there is no doubt that the book is a guidance for those conscious of Allah, those who pray, give Zakkah etc.. The first part of the chapter talks about Muslims, and gives the good news to Muslims and how they'll be the inheritors of success in the hereafter, then if you read along, it starts talking about none Muslims,

2:13 And when it is said to them, "Believe as the people have believed," they say, "Should we believe as the foolish have believed?" Unquestionably, it is they who are the foolish, but they know [it] not.

Then if you continue reading along, Allah (swt) talks to the whole of mankind:

2:23 And if you are in doubt about what We have sent down upon Our Servant [Muhammad], then produce a surah the like thereof and call upon your witnesses other than Allah , if you should be truthful.

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All the major religions ask for sincerity - and this is true for Islam itself - in order to free one from doubt; they also remind people that those who display the outward signs of religion may not be inwardly sincere.

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