Cause, Effect, or Affect?

The following may not have much coherence or make much sense, but please bear with me. I am thinking "out loud".

I heard a speaker the other night say that, since Jesus has authority over all of history, he caused the bad things that happened, including the 9/11 attack on the World Trade Center. Does God cause bad things, or does he allow them to happen? And if he allows them to happen, does that mean that he is not in complete control? Are the bad things things that God does since he controls everything, or are they the result of the evil in this world and our fallen, sinful human nature? The Bible says that God works things out for the good of those who love Him, but does that mean that he takes the bad situations that we cause and uses them for good, or does that mean that he causes the bad things and still uses them for good? A god that caused bad things to happen to the people he created does not seem like a very loving god, but more like a child with a magnifying glass killing ants on a sidewalk for the fun of it. There are also situations where something that we perceive as being bad at the time ends up being a very good thing when we look back on it, although perhaps not something that is on the same scale as the World Trade Center attack. Are large scale "bad" things viewed differently by God than things that we see as being on a smaller scale, such as loosing a job or a loved one?

Genesis 50:20: "You intended to harm me, but God intended it for good to accomplish what is now being done, the saving of many lives." That is what Joseph said to his brothers after they sold him into slavery and he ended up being able to save all Egypt from being victims of a terrible famine. Did God make the brothers sell Joseph, or did he just use the situation without causing it in the first place? If he made the brothers sell Joseph, doesn't that mean that he didn't allow them free will?

When Job is suffering from intense illness and the loss of his children and all his possessions, his wife comes up to him and tells him to "Curse God and die!" Job replies, "You are talking like a foolish woman. Shall we accept good from God, and not trouble?" (Job 2:10) In Job's story, God does not cause the bad things that happen to Job, but instead allows the devil to do them to Job, with set limitations. Is this how things really happen? If so, the devil influences people, and not God, to do bad things and God allows them to do those things. However, people still have the ability to make the choices for themselves and have free will and can only be influenced.

God could cause things to happen that influence our decisions by influencing the decisions of others in a very complicated web of influence and decision making. But he would also know what those decisions ended up being in advance since he is beyond the restraints of time. I once heard it said that when we make a choice to follow God, it is like us choosing to open a door and God is on the other side saying "I have chosen you." So does God use our choices, and causes things to happen that make these choices work out the way he wants them in the end?

It is all very confusing...and I think my brain is about to explode. I think it is safe to say that God is much bigger than I am, and it is a good thing that he understands everything, because I definitely don't.