I may not respond to each of your inquiry but only the ones I feel I should.
You interpret and think similar to the way the lost souls do. The lost souls - the ones the west calls the "terrorists"! All out of context, out of historical context, out of socio-cultural context!
Quran can be divided into two parts...
A) A book or rules
B) A historical document
If you are reading a part that is narrating a historical event - then you have to understand the historical context. You cannot inexpertly take out a verse from the historical narration and randomly try to apply to all future settings and scenarios. That is a no no!
It is better for you to concentrate on the verses that apply to all times and easy to understand. There are countless verses in the Quran that shows you the path to perfection, the path to glory, path to peace and harmony.
Concentrate on those parts first!
The parts that you are concerned about - seek and find proper scholars who are learnt both historically and linguistically.
Wrong!
Apparently this verse was revealed during the initial recruitment period to preserve the teachings of the Quran. Try to understand the setting! It would be difficult for you sitting somewhere comfortably in this century, but try, I give you an example you may be able to relate to.....
Go to a biker's bar and declare drinking alcohol is a sin, riding a bike is a sin, wearing tattoo is a sin and see what happens to you.
Afraid to go alone? Try and find some recruits to go with you.
You will fail!
Being a prophet is not an easy job! Especially when you decide to not use miracles to convince people. Jesus used miracles. It kind of backfired! People started believing he was son of god!
There is a third choice! You could be a Muslim by faith and yet fooled into believing you are doing the right thing out of desparation or via misguidance.
Killing innocent is wrong but they could justify it within their head by misguidance by their leaders. Sometimes - peer pressure makes people do the wrong thing as well.
A couple of bad apples could be responsible to make the entire basket rot.
When you are looking for a solution to your everyday problem - you use whatever tool you find and worry about consequences later!
For us (me and you) sitting far away from all that - it is easy to say - they were wrong!
And of course they were wrong!