People look at women being mistreated in the Muslim world and say "oh it's because of Islam's scriptural content regarding women," but it's really not. This mistreatment stems mostly from non-Islamic cultural roots and from the activities of conservatives/extremists pushing ideas that aren't in the Qu'ran.
First of all, I respect your opinions, and by and large I agree with them. As for the original post, the shootings at Fort Hood seemed to have nothing to do with the soldier's religion at all and probably were the result of unresolved emotional issues because of the shooter's tour of duty. I agree that Islam is being unfairly pointed to as a cause for this crime; it's too bad that idiot had to scream "Allahu akabar" before opening fire.

That said, I don't know the contents of the Qu'ran, so I will not comment on it but give you the benefit of the doubt, especially considering how violent the Tanakh (more specifically the Torah) can be as you pointed out above. However, as you say, the common conduct of members of a religion is just as much a part of the religion as strictly what is canonical or doctrinal.

Regardless of what is stipulated in the Qu'ran or whether Jihad is defined as a more metaphysical struggle rather than a truly military one, there is something fundamentally wrong with modern Islamic culture. Unfortunately, the reality is that Muslims with moderate attitudes regarding their faith, tolerance of other religions, and who believe in non-violent resolutions to conflicts are in the minority.

That's not to say that there aren't perverse practices justified through religion amongst adherents to other faiths. But none are so widespread as they are in Islam.

Just take a look at countries ran by Muslims. Most of them cannot separate church and state. As my father said who taught English in Saudi Arabia for a year, there the Christian Bible is (or at least was) treated the same way as pornography. Turkey is secular through a rather brutal enforcement of social secularism. Even Malaysia, the largest Muslim state with a rather religiously diverse population, forces all ethnic Malayas to submit to Shrariah law, and the Shariah courts rulings can countermand any ruling from a secular court.

The latest "Islamic state" is Chechnya, where a Muslim was elected as president of this constituent state of Russia. At first the Kremlin was quite supportive of him, as they looked upon him as someone who could bring peace to the region and solidify Russian control of the region. Now, he's forcing all women to wear Hijab, supports honor killings, and is otherwise stripping Chechnyans of their human rights in the name of Islam.

Sure, in India, there are Hindu extremists. There are Hindu terrorists. There was even some legitimate cause for concern when a party with Hindu fundamentalists leanings had controlled the central government for a time. But India is still at its heart a secular democracy, with free religious expression and an open society. The current prime minister is, in fact, a Sikh and not a Hindu (and by and large a very good leader). Pakistan, on the other hand, is a hotbed of Islamic extremism with an small educated population under siege by a larger population of poor uneducated people leaning towards extremism and a military that often supports militant fundamentalism against the wishes of its civilian government. There is little tolerance for practice of any religion other than Islam. Pakistan is poorer than India, yes, but before the partition of these two states Lahore was a cosmopolitan and diverse city.

So in sum, there is something undeniably and systemically wrong with modern Islamic culture. We're far from the days of the highly enlightened Moghul court that had both practicing Muslims and Hindus among its members (though officially Muslim itself).