Thanks AbaAbdillah for trying to answer my questions and I feel that you are honest in doing so.
1) Concept of hell for eternity does not seem fair. Though one explanation is that it will appear like eternity due to level of suffering. Even then is this fair.
From my own Islamic understanding and conclusion. Satan when he argued with God against his decision of preferring humans to him, he refused to bow to Adam and became cursed (meaning God removed His Mercy for satan) rather than satan repenting, his own arrogance made him challenge God that he would prove that we are not worthy of that preference and that he could easily turn us away and make us disbelief in Him and show Him ingratitude.
So God replied that whoever agrees with Satan will end up with him, i.e in hell.
As for an eternity. All the ones who as the hadith says have a "mustard seed of faith" in their hearts will eventually be taken out of hell fire. But the ones who disbelieve in God completely, they will have God's Mercy removed, so therefore they will abide there permanently.
Also keep in mind, that a person has to be sane to make a decision, and has to have had Islam reach him/her in a convincing way and not in the repulsive way that it is shown today, not only in the media, but by ignorant Muslims who have no manners. People of fitrah (e.g people in the amazon) and the people who have not heard anything about Islam, and even the ones murdered who weren't allowed to live out their full lives, I am more than certain of God's Mercy, that he will take all situations into account, and God knows best.
From Quran 2:30:
And [mention, O Muhammad], when your Lord said to the angels, "Indeed, I will make upon the earth a successive authority." They said, "Will You place upon it one who causes corruption therein and sheds blood, while we declare Your praise and sanctify You?" Allah said, "Indeed, I know that which you do not know."
The angels said this before Satan rebelled against God. This can mean two things:
1) God made man to commit sins (causes corruption therein and sheds blood) even without Satan misguiding them
2) Even angels knew before hand that Satan will rebel and will cause many humans to suffer hell fire for eternity. Further why would God create Satan knowing that this creature will rebel against its own creator.  
So God created Satan to misguide people in to hell fire and then sent vague guidance to SOME of the humans in a limited area to save them. Apparently God gave Satan more advantage in achieving his objectives.
2) Slavery and allowance of intimacy with female slaves
This was something that was practiced in all places in the pre-modern world. The ones that lost in a war, their families became slaves of their victors. It was all very common in those times and largely accepted, even the Prophet Abraham in the Bible was quoted as having a slave girl. Galatians 4:22 "For it is written that Abraham had two sons, one by the slave woman and the other by the free woman." From my understanding these things no longer apply. And if Muslims apply that today, then they shouldn't complain about the way their women are treated in warfare.
It is quite a delicate topic that needs alot of expansion, I do not know too much about it, I will wrap it up by quoting what Muhammad (SAW) said "“If any of you have a slave girl, whom he gives good education and excellent training, and then he emancipates her and marries her, he shall have a two-fold reward.”
There are many counter arguments to this like there were many other things common too but were abolished by Islam.
However I would just like to ask one thing. Suppose Islamic government the way it should be is established in modern time. Then there is a war between muslims and non muslims.  Muslims capture female soldiers who are non-muslim.
They are distributed as booty to muslim soldiers such that each soldier gets 3 each
.
The muslim soldiers have sex with these captives as it is allowed by Quran. Even consider for some odd reason these women also agreed to do so though they were married.
Now in this situation considering it is say 2015, will you say the Muslims soldiers had the right to have sexual relationship with three different women without marrying them? Remember you can not make unlawful for yourself what God has made lawful for you.
3) Why is Quran not structured to be clearly understood without any doubts if it is guidance for all mankind
It was a revelation that was revealed in a certain time and understood in a certain context. If you wish to understand it, you have to look at every particular verse and why it was revealed and in what context. Most of what came down was a response to questions posed to the Prophet(SAW), or addressing a certain situation, or confirmation of old stories and scriptures to bring converts from among the Christians and Jews and to purify their teachings.
The Quran is not intended to be read as a story but looked at as a book of lessons. In life you will learn by experience, parables, events, metaphors (if you still don't get the point) and knowledge.
So it will give you some knowledge of the unseen, tell you stories to draw lessons, and give you metaphors and it will address some questions.
That is why I hate the approach of people like Zakir Naik and Harun Yahya. I do not agree with trying to use the Quran as a book of scientific Miracles by stretching some verses far out of context, with all due respect to them.
Although I believe that there is truthful science in the Quran, some I can think of, the speed of light, the barriers between seas and rivers, embryology, the big crunch, the big bang...  
Agree that Quran is intended to be a book of guidance. And it also claims to be clear guidance for all humanity and time.
Is it structured or written to fulfill these two objectives as effectively as divinely possible?
If you prove to me that it is to be understood in the light of hadith only, then this will mean (to me) that Quran is not authentic as I do not trust hadith anyways. I am saying this because you mentioned time and context. And from typical understanding of muslims time and context comes from hadith. So in this case I will need to trust hadith collection to understand Quran. If I trust sahih hadith collection to be authentic then it means end of Islam (for me) because many hadith cast shadow of serious doubts on the personality of prophet and other companions.
4) I can not digest the part where Quran mentions that Allah guides who he wants and let others go astray. And did Allah create human so that he can have most of them burn in hell for eternity.
What is meant is that, the person has to want that guidance, a quote from the Quran says "He misleadeth many thereby, and He guideth many thereby; and He misleadeth thereby ONLY MISCREANTS; Those who break the covenant of Allah after ratifying it, and sever that which Allah ordered to be joined, and (who) make mischief in the earth: Those are they who are the losers." 2:26-27
No person is just doomed, every person has a chance to change their lives around. How many people have you seen who were the worst "sinners" whether they be average people, or celebs, who have turned their lives around completely and became religious.
Just read up on Malcolm X
Refer to the first question. I can expand more, but I am trying to be brief.
Who will not want guidance? Can a sane person who thinks there might be God say that he/she does not want guidance?
5) The theory of evolution makes a lot of sense to me. However it does not seem to be compatible with Islam unless we do not take the story of Adam and Eve to be literal.
I believe in evolution. Adam and Eve (As) were according to some hadiths 90 feet. Some ignorant Muslims have tried to show that the first human was 90 feet and use hoaxes on the internet for their proof, which is cringeworthy. The reason why I mentioned that, is because in Islam, in the afterlife we will have different bodies. Now 90 feet was the height of Adam (AS) in PARADISE and not on earth, because he was removed from paradise and sent down to the lowest heaven along with Eve (As) and satan.
So in the hadiths it appropriately says that the occupants of hell and paradise will have different bodies, and that the occpuants of paradise will be 90 feet and that the occupants of hell will have skin that keeps healing and extremely wide shoulders to feel excess pain, which sounds terrifying and rather harsh (I admit).
Now which brings me to my actual point!!! How do we know that after Adam (As) was thrown out of paradise his soul was not placed in the first man that was created out of evolution?
Can that possibility be ruled out scientifically speaking?
And it might interest you to know that Muslim scientists such as Ibn Khaldun, al Jahiz, Nasir al din al tusi, al Biruni and many more came up with the theory of evolution long before Darwin hopped on the bandwagon.
Ibn Khaldun said in his book Muqadimmah "The higher stage of man is reached from the world of monkeys, in which both sagacity and perception are found, but which has not reached the stage of actual reflection and thinking. At this point we come to the first stage of man. This is as far as our (physical) observation extends"
http://www.muslimphilosophy.com/ik/Muqaddimah/Chapter1/Ch_1_06.htmThere is in fact reverse evolution in Quran too. God turned Jews in to monkeys. What do you say?
On a serious note if a book mentions turning Humans in to monkeys then do you seriously think it is fair to associate evolution with Adam & Eve story?  Without having any reference to evolution in Quran.
I do like your explanation though.  
6) Various events like the Nuh's flood as mentioned in Quran appear like fairy tales. Some how I can not digest these miracles now. I did not think about it earlier.
Even an atheist friend who I work with concedes that a flood did occur of what is talked about in the Bible and Quran, but he doesn't believe the accounts that they give. The Bible says it was worldwide, the Quran says local. People weren't living on other continents at the time due to them not being discovered, so I disagree with the Bible.
If it was a local flood then why did Nuh bother to make the boat. He could have moved to safer grounds with all of his followers and animals etc
7) There is no ideal muslim society to look up to. What is the use of teachings which are not effective in real life. The political mess started right after death of prophet Muhammad in early years of Islam e.g. War of the camel.
You'll have to explain what you mean, as for your latter point, it is never going to be perfect after the Prophet (SAW). Yes there were many civil wars that occured and disagreements, but this is a human problem it's never going to go away. I take it that you might be a Shia, because I do not believe that the political mess started right after the death of the Prophet (SAW), so I disagree with that point.
And you have to look at what the Muslim world achieved, not just the negative parts. Religion is not immune to being hijacked by corruptive rulers. Many Muslim rulers have been extremely barbaric.
You should also look at the expansion of the Muslim empire:
http://en.wikipedia.org/wiki/Islamic_empireAlso read about the al andalus:
http://en.wikipedia.org/wiki/Al-AndalusRead about Muslim scientists:
http://en.wikipedia.org/wiki/Muslim_scientistsI agree that there are alot of problems right now in the Muslim world and have been so for a very long time, but you should also look at what good has come out of Muslim civilisation, otherwise you're not being objective. And bottom line is human beings are always going to have flaws.
I was never a Shia. I was born in non-Shia muslim family. However my family never associated with any sect.
Anyways what about the war of Camel? Did it not happen between Ali and Aisha? They were two of the closest people to Prophet and must have understood his teachings better than many other.  
Secondly suppose if you need to get 4 out of 10 questions right to pass. You only score 3 right answers. Your status is failed even though you did give some right answers.  So even if there are few positives over 1500 years does not mean much.  Is there any overall successful example of Muslims following Islam?
BTW I do not know...may be Malaysia, Indonesia, Turkey? Does any one know if they can be considered good example of Muslim society.
Another point is that if God wanted to propagate  Islam and convince non-muslims, an ideal muslim society would have been much more effective than a book claiming to be perfect without any living example of its divine guidance in effect socially.
Topic: Hi from on the fence muslim