No matter how much you 'know your stuff' or how long you have walked with Him or how many questions of your own He has answered, your spirit will be troubled.
No matter how many prayers have been answered (beyond the range of statistical probability) or how much character transformation you have personally experienced (beyond the range of self-help methodologies) or how many skeptics you have seen come to trust this Living Lord, your spirit will be troubled.
God has not answered all of our questions, and for his own reasons. He meets our needs, many of which are intellectual, but He just doesn't seem to answer them all. You can raise more questions in 5 minutes than you can answer in 500 years.
Deut. 29:29:The secret things belong to the LORD our God, but the things revealed belong to us and to our children forever, that we may follow all the words of this law.Most of the questions and issues they raise have already been answered in many ways, and in many generations. But SOME that they raise may never be answered--in this life or the next. (Some may not even be real questions, actually...but that's a philosophical issue for another time.)
I learned a long time ago that God is not embarrassed about a single verse in the bible (but I have been) and that He is not afraid of any question of truth that a person can raise (but I have been). He really, really, really is a God of truth and honesty and goodness.
Doubt can be a important step in learning how powerful our God is, and how firm his 'case' is...but doubt, like any need of ours, must be brought to Him for His action. Our questions are typically His tools in our lives--to teach us to trust him, to be patient, to be fearless, to be honest, and to be diligent and humble in study. They can be answered quickly (in seconds) or in agonizing slowness.
God's vindicates His own story, in a surprising number of ways(!) in the lives of people. Our job is simply to be honest and forthright and loving.
Speaking the truth in love, we will in all things grow up into him who is the Head, that is, Christ. (Eph 4.15)A wise old Bible teacher once told a story of a bright, young student who was worried about losing his faith over some Bible difficulty he had been agonizing over for some time. The professor kindly admonished the student with a simple "Son, why are YOU trying to hold the ROCK up, instead of letting the ROCK hold YOU up?!"
Now before you charge off, don't forget to check the "Ethical Vectors" list, to make sure you re-calibrate your attitude around the boundary conditions.
And, as always, if you have any questions about what you see, send them to me at firstname.lastname@example.org