What in Quran disturbed me as a muslim ?

1) Verses in Quran about torture for shirk/kufr in hereafter [hell]

I never got the point that why shirk/kufr deserves infinite punishment . It is a harmless act . If it is a crime , then who is the victim of it ? is it allah ?

Following are the very few verses out of too many horrible verses.

40:71-72 – When the shackles are around their necks and the chains; they will be draggedIn boiling water; then in the Fire they will be filled [with flame].

22:19-21 – These are two adversaries who have disputed over their Lord. But those who disbelieved will have cut out for them garments of fire. Poured upon their heads will be scalding water; By which is melted that within their bellies and [their] skins ; And for [striking] them are maces of iron. 

4:56 – Indeed, those who disbelieve in Our verses – We will drive them into a Fire. Every time their skins are roasted through We will replace them with other skins so they may taste the punishment. Indeed, Allah is ever Exalted in Might and Wise.

56:92-94 –  But if he was of the deniers [who were] astray; Then [for him is] accommodation of scalding water; And burning in Hellfire

8:55 – Indeed, the worst of living creatures in the sight of Allah are those who have disbelieved, and they will not [ever] believe –

98:6 Indeed, they who disbelieved among the People of the Scripture and the polytheists will be in the fire of Hell, abiding eternally therein. Those are the worst of creatures

4:52 – Those are the ones whom Allah has cursed; and he whom Allah curses – never will you find for him a helper.

4:47 – O you who were given the Scripture, believe in what We have sent down [to Muhammad], confirming that which is with you, before We obliterate faces and turn them toward their backs or curse them as We cursed the sabbath-breakers. And ever is the decree of Allah accomplished. 

5:60 –  Say, “Shall I inform you of [what is] worse than that as penalty from Allah ? [It is that of] those whom Allah has cursed and with whom He became angry and made of them apes and pigs and slaves of Taghut. Those are worse in position and further astray from the sound way.”

2) Genocide commanded by god to the people of moses

People of Moses worshiped a calf , so god ordered them to kill each other in repentance. This sounds like a god of hindus who need human sacrifice to show mercy or to bless 

2:54 And [recall] when Moses said to his people, “O my people, indeed you have wronged yourselves by your taking of the calf [for worship]. So repent to your Creator and kill yourselves. That is best for [all of] you in the sight of your Creator.” Then He accepted your repentance; indeed, He is the Accepting of repentance, the Merciful.

Tafsir Ibn Kathir
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An-Nasa’i, Ibn Jarir and Ibn Abi Hatim recorded Ibn `Abbas saying, “Allah told the Children of Israel that their repentance would be to slay by the sword every person they meet, be he father or son. They should not care whom they kill. Those were guilty whom Musa and Harun were not aware of their guilt, they admitted their sin and did as they were ordered. So Allah forgave both the killer and the one killed.” This is part of the Hadith about the trials that we will mention in Surat Ta Ha, (20) Allah willing.Ibn Jarir narrated that Ibn `Abbas said, “Musa said to his people, ﴿فَتُوبُواْ إِلَى بَارِئِكُمْ فَاقْتُلُواْ أَنفُسَكُمْ ذَلِكُمْ خَيْرٌ لَّكُمْ عِندَ بَارِئِكُمْ فَتَابَ عَلَيْكُمْ إِنَّهُ هُوَ التَّوَّابُ الرَّحِيمُ﴾ (“So turn in repentance to your Creator and kill each other (the innocent kill the wrongdoers among you), that will be better for you with your Creator.” Then He accepted your repentance. Truly, He is the One Who accepts repentance, the Most Merciful.) Allah ordered Musa to command his people to kill each other. He ordered those who worshipped the calf to sit down and those who did not worship the calf to stand holding knives in their hands. When they started killing them, a great darkness suddenly overcame them. After the darkness lifted, they had killed seventy thousand of them. Those who were killed among them were forgiven, and those who remained alive were also forgiven.”

3) Horrible punishment [lashing / stoning] for fornication/adultery

 24:2 The [unmarried] woman or [unmarried] man found guilty of sexual intercourse – lash each one of them with a hundred lashes, and do not be taken by pity for them in the religion of Allah , if you should believe in Allah and the Last Day. And let a group of the believers witness their punishment.

Tafsir Ibn Kathir
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Then Allah says:

﴿الزَّانِيَةُ وَالزَّانِى فَاجْلِدُواْ كُلَّ وَاحِدٍ مِّنْهُمَا مِاْئَةَ جَلْدَةٍ﴾

(The Zaniyah and the Zani, flog each of them with a hundred stripes.) This honorable Ayah contains the ruling on the law of retaliation for the person who commits illegal sex, and details of the punishment. Such a person will either be unmarried, meaning that he has never been married, or he will be married, meaning that he has had intercourse within the bounds of a lawful marriage, and he is free, adult and of sound mind. As for the virgin who is unwedded, the prescribed punishment is one hundred stripes, as stated in this Ayah. In addition to this he is to be banished from his homeland for one year, as was recorded in the Two Sahihs from Abu Hurayrah and Zayd bin Khalid Al-Juhani in the Hadith about the two bedouins who came to the Messenger of Allah . One of them said, “O Messenger of Allah, this son of mine was employed by this man, and committed Zina with his wife. I paid a ransom with him on behalf of my son one hundred sheep and a slave-girl, but when I asked the people of knowledge, they said that my son should be given one hundred stripes and banished for a year, and that this man’s wife should be stoned to death.” The Messenger of Allah said:

«وَالَّذِي نَفْسِي بِيَدِهِ لَأَقْضِيَنَّ بَيْنَكُمَا بِكِتَابِ اللهِ تَعَالى، الْوَلِيدَةُ وَالْغَنَمُ رَدٌّ عَلَيْكَ، وَعَلى ابْنِكَ جَلْدُ مِائَةٍ وَتَغْرِيبُ عَامٍ، وَاغْدُ يَا أُنَيْسُ لِرَجُلٍ مِنْ أَسْلَمَ إِلَى امْرَأَةِ هذَا،فَإِنِ اعْتَرَفَتْ فَارْجُمْهَا»

(By the One in Whose Hand is my soul, I will judge between you both according to the Book of Allah. Take back the slave-girl and sheep, and your son is to be given one hundred stripes and banished for one year. O Unays — he said to a man from the tribe of Aslam — go to this man’s wife, and if she confesses, then stone her to death.) Unays went to her and she confessed, so he stoned her to death. This indicates that if the person who is guilty of illegal sex is a virgin and unmarried, he should be banished in addition to being given one hundred stripes. But if married, meaning he has had intercourse within the bounds of lawful marriage, and he is free, adult and of sound mind, then he should be stoned to death. Imam Malik recorded that `Umar, may Allah be pleased with him, stood up and praised and glorified Allah, then he said; “O people! Allah sent Muhammad with the truth, and revealed to him the Book. One of the things that was revealed to him was the Ayah of stoning to death, which we have recited and understood. The Messenger of Allah carried out the punishment of stoning and after him we did so, but I am afraid that as time goes by, some will say that they did not find the Ayah of stoning in the Book of Allah, and they will go astray because they abandoned one of the obligations revealed by Allah. Stoning is something that is prescribed in the Book of Allah for the person — man or woman — who commits illegal sex, if he or she is married, if decisive evidence is produced, or if pregnancy results from that, or if they confess to it.” It was also recorded in the Two Sahihs in the lengthy Hadith of Malik, from which we have quoted briefly only the portion that is relevant to the current discussion