A man known for his honest doubt, Thomas, one of Jesus' disciples, eloquently expressed his doubts concerning Jesus' resurrection. He blurted, "Unless I shall see in His hands the imprint of the nails, and put my finger into the place of the nails, and put my hand into His side, I will not believe." These were strong conditions, but they were clear criteria for truth.
There was a willingness to honestly investigate the evidence for the event and follow-through with belief.
These kinds of questions and doubts, God welcomes, encourages and answers. If you are a seeker, you can ask any question you want and you will find adequate answers. History is filled with men who asked questions about God. They asked the questions of seekers, meaning although they doubted, they would be willing to believe if God would show them the truth.
History is also strewn with the questions of brilliant men who did ask fine questions but found heaven constipated. There were no answers to them, not because there were no available answers, but simply because they asked as skeptics. They doubted too, but were unwilling to believe.
Doubt, my friend, is not unbelief nor faulty in itself. Only dishonest doubt will not find an answer, for there are no questions that can be asked which have not been asked before. And, there are no questions that can be asked which have not been asked and answered before!
Don't be afraid to ask questions about God, truth and reality.