Some of the questions are semantically ambiguous and the answers are too restrictive to exactly represent my philosophy.
My apparent moral conflicts were concerning objective morality and the evil of genocide, and preventing unnecessary harm to to the environment and letting people journey by car.
The first conflict was half a result of me substituting the term 'evil' for 'something generally negative to survival', and half taking the generally perceived opinion of evil as an overall definition of evil so that I could actually give an answer to the question. If the question had specified objectivity, then I would have had no problem answering it.
The second is me being pedantic in my definition of the word 'unnecessarily' and what constitutes 'the pursuit of human ends'. If someone wants to travel from A to B with the speed and flexibility of driving a car (the human end), then it is inherently necessary to cause the resulting pollution.
When I agreed that unnecessary damage to the environment was bad, I was referring to the act of, whilst going about your task, doing something that would cause or contribute to significant damage, that also does not proportionately contribute to the completion of this task. One could argue that this does not fully constitute damage 'in the pursuit' of something as it is clearly not connected to the success of the activity. I would say that doing something 'in the pursuit' of something else only implies intent to do something, not the competence to do it correctly, which could easily lead to unrelated activity being included in the pursuit of something else.
Either way, I know most of my philosophy's weak points and these questions did not highlight any of them. Mostly it comes down to ideal VS reality and reality generally wins because that is where most of us are living at the moment. Sure it would be nice if everyone was free to do what they wanted, but in reality that heroine addict injecting himself in front of your family is almost certainly a detriment to you and society in general and in the end, society comes first.
Also a slight aside, but my view on atheism is less of a "NO, THERE IS NO GOD!!" (excluding our friends the militant atheists of course) and more, for example a Theist saying "Hey! So there's this God guy, right?" and the Atheist replying "What? That doesn't make any sense, I'm going to continue as I was and ignore this.". The first is an active denial of something, the second shows the theist as the active party, the atheist responds to the input given with the information and reasoning available. The difference is subtle, but I think it is significant. I don't see myself as someone who is denying something, I just don't really recognise God as something worth considering the existence of and if it weren't for theists introducing the concept into my world, I wouldn't have to.
The distinction between this and an agnostic, to me, is just that an agnostic is either an atheist who hasn't thought enough about it to claim to be one, or a non-committal theist who doesn't want to fully invest in faith for whatever reason.