My Dear Friend,

I read your post and after reading it i felt there are a lot of other things that you need to know. In fact i think if i was you i would have reacted the same or maybe worse after reading those suras. However the key thing before reading any sura is to know its context. These suras were sent down according to circumstances at that time. They are reffering to particular incident at that time. For example you quoted “God does not love those who overstep limits. Kill them whenever you encounter them.” This phrase is not for us to follow in this time but for those at that who were warned over and over not to cross the limits of God but they did. Again this doesn’t mean Islam or Quran offers violence. Its just the context that we have to follow before coming to any conclusions. We can not just pick a line from Quran and say, see this is what Islam is all about or quran preaches this or that. There is a complete story and consequences behind it. Unfortunately there are few extreme Muslims out there who do the same thing. They pick one line from anywhere in the Quran or Hadith and start following it. To me this is complete ignorance.

As far you are concerned about Quran’s treatment with Jews and Christians. Again its the same thing. Its that particular context in that Sura. God does say in the Quran whoever believes him, he or she will get its reward regardless of their religion (Jews, Christians etc.) If you read about Prophet Muhammad life, you will find his treatment with Jews and Christians as equal as Muslims. 

My sugestion for you is to read “In the footsteps of Muhammad”. I am sure you will find a lot of the answer to your questions that you mentioned in your post.