What is the Truth behind violent verses of the Quran?

Militants and terrorist say they are following the Quran in word and spirit, that they are the best of the believers in imitating the Prophet, who is referred to as the best example to follow. 

The verses of the Quran from Mecca are peaceful. The verses in Surahs of Medina have violence. 

Medina is of a later time period when the prophet moved from Mecca to Medina, where an increasing number of tribal warlord type battles were fought. 

You can Google violent verses of Quran and find those chapters (Surahs) are from Medina. 

The problem is that Quran states that later (violent) verses overrule the earlier (peaceful) verses if they are contradictory. 

The context of these verses is given in the stories narrated in the Hadiths (books) to make sense of them.

There are many powerful tribal warlord type offensive battles/conquests described in the Hadiths of the Prophet’s life in Medina, in addition to the defensive battles with the Quresh of Mecca. Lookup Banu Qurayza - the massacre and beheadings of Jews supposedly by the Prophet and his commanders. 

But was it the Prophet who went on these attacks or were the descriptions of his generals who later became the Caliphs (Muslim ruler)?

I know that angel Gabriel, as a messenger of a loving God; and the pious, humble, devoted, peaceful, and pure Prophet, could not have conveyed these "kill them", "strike them on the neck" verses, no matter what the context or interpretation (which is generally blamed). In my understanding, a just and loving God, does not torture, punish and condone massacres, it is man who uses the name of God to justify his own evil. 

The Caliphs were conquerors and used religion, i.e., Islam, to increase their power. The 3rd caliph many years after the Prophet got the Quran and Hadiths compiled. Till then the verses and stories were all verbal. There is no proof of the original verses and stories being converted to written form accurately. It is only a belief passed down over hundreds of years and the truth may have been lost. Recently many versions of the Quran's manuscript were found in Yemen, and elsewhere.

Ali compiled a complete version of the Quran, mus'haf, six months after the death of Muhammad. The volume was completed and carried by camel to show to other people of Medina. The order of this mus'haf differed from that which was gathered later during the Uthmanic era.

So it confirms that the verbal word could not have been converted exactly into written word, there are contradictions in the manuscript versions found. It's available online. The 3rd Caliph, Uthman, was very keen on converting the verbal form into a cemented written form which he repeatedly used to justify his violent conquests and oppression. Imam Ali, (the spiritual head of Islam, the son-in-law of the prophet, and the 4th Caliph) often opposed the Caliph saying that it was not said by the prophet nor were these violent acts condoned by any word of God. 

The problem is that many militants and terrorists today act very similar to the Caliphs and their army. They quote these violent verses of the Quran, and justify their actions from scholarly interpretations, and stories of the Hadiths of the Prophet who went on wars. But are they following the Prophet or some commander? Was the Prophet's name used in place of commanders?

As you know the Bible was changed by Constantine to use religion for his power and conquests.

Quran states that the Bible was changed, and therefore no one can touch a single letter of the Quran, Hadiths, or Sharia (Muslim law). Separately, shouldn't constitutions and laws that govern man be amendable, and changeable according to time and place? Would we want laws from the dark ages unchangeable and applied to this century or would we want laws to change as man evolves?

I believe the Prophet was peaceful and loving. The generals and Caliphs were violent and used religion for power. My findings have led me to believe that the peaceful verses alone were the word of God. 

Ameen