There are parts of the Bible I find hard to believe and hard to stomach, and I do not want to just bury that. What do I do with those passages?

“Open thou mine eyes, that I may behold wondrous things out of thy law.”

This psalm is a long, patient meditation by someone under real pressure who keeps returning to God's word. The line is a prayer said before reading rather than after understanding. It assumes a text can sit in front of you fully open and still be closed to you, and that the remedy is asked for rather than achieved. That is a workable posture for hard passages.

“All scripture is given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness: That the man of God may be perfect, throughly furnished unto all good works.”

Paul writes to a young pastor facing teachers who twisted scripture for profit, and he is describing what the text is for as much as where it came from. The uses he lists are all practical: teaching, correcting, training. A book that exists partly to correct you will contain material that resists you. Difficulty is not automatic evidence that something is wrong.