I remember those times, too. I would get angry with him about something in my life, but I would feel comforted, as if he understood me, and that he would stay by my side. Whatever hardships I personally had with god, despite making me a bit angry or frustrated with him at times, never made me question him. The point at which it started to unravel was when I expanded my world from just "me me me" and started being angry at god for others. I couldn't simply be angry at god, have my words with him, have him comfort me, and have that be over with. I would be angry with god about something outside of me, things I saw being done to others I loved or cared about, then I would have words with god, and after seeing nothing be done or changed, things would stay unresolved, and I would be left with nothing but more questions.
Then why could you not just pray for others and realize that they are on their own journey as well? Pray that God could help them make sense of the horrible things they had to endure? Yes, I know a bit about your story. Perhaps you have had to go through more than most do for sure, and your heart is so big and filled with so much compassion that it makes it even more difficult to stand by and see others suffer. But have you considered that perhaps that "big heart" of yours was put there by God? He is the one that puts love in our hearts. He has an amazing way of turning the crap we have to go through into something amazing if we just let Him, or ask Him too.
And I think it is OK to question. We should question. I still question Him. The difference is that I have come to realize that in my finite mind I will not be able to understand everything and I have learned to trust God regardless of that. There are going to be things in this life that make absolutely no sense at all, and perhaps God is waiting until after life to make some of those things right? I do believe that He has put fairness into our hearts and our sense of "justice" comes from Him. So whatever does not seem right or fair or just, just let Him know. He wants us to be direct and honest. He certainly can handle it.
I guess what I often see if that people get so ticked off at God that they want to blame Him for not doing anything about the problems in the world. I often feel like He does choose to stand by on the sidelines and just watch. But then I have found the reason He is not involved in our lives is because we have not asked Him to be, or we don't want him to be involved. Our own pride makes us want to do everything on our own without Him. And He completely respects that and lets us have our own way, regardless of how much more difficult it is on us, and even on Him. I think it does hurt Him when He sees us suffer so much.