Jihad- At least the one pertaining to physical fighting can be clarified easily by reading the Qur'an, which is conveniently forgotten by extremists and retarded bigots alike.
The Quran teaches that when war breaks out, it should be waged in such a way as to cause the least possible amount of damage to life and property; and that hostilities should be brought to a close as quickly as possible.
"22:40 Permission to fight is given to those against whom war is made, because they have been wronged - and Allah indeed has power to help them - "
This is basically stating that a just war is only permissible when it is declared in defence of aggression, not the fairy tale invented by Mullahs or Faux News.
"22:41 Those who have been driven out from their homes unjustly only because they said, 'Our Lord is Allah' - And if Allah did not repel some men by means of others, there would surely have been pulled down cloisters and churches and synagogues and mosques, wherein the name of Allah is oft commemorated. And Allah will surely help one who helps Him. Allah is indeed Powerful, Mighty - "
Can a verse be more clear? It is clearly stating that a true jihad is one that defends the sanctity of religions and their worship places. There is no distinction being made between defending mosques or defending churches.
Female Genital Mutilation -cultural practise followed by Muslims, Christians and pagans. Nothing to do with Islam. No justification, another story of cultural practises being adopted by people who changed their religions but kept their old customs.
Stoning - No punishment of stoning proscribed for any crime in Islam.
Suicide Bombing - “And do not kill yourselves. Surely, Allaah is Most merciful to you.” [Surah Nisaa 4:29]. No need for more clarification.
Islam and Science - Really? Anyone who has studied early medieval Islamic history knows that Islam places no restrictions on Science. No contradiction, never have I read anywhere that the pursuit of Sciences is Haram.
Now I know what the people will say, that what is happening is different to what I have stated. I agree, Muslim world needs reforming and honest political and religious leadership. The Muslim world currently is where Europe was just before the renaissance, give it time. The Christians wiped out a quarter of their population not more than 300 years ago due to sectarian infighting. It is a natural progression.