No, I never said don't question it. Question everything you don't understand. I had some of these same issues years ago, but learned a lot of the background information in college in Old Testament and Ancient Scripture courses. I recall hearing about one extrabiblical account of Enoch speaking to the Lord and when the Lord tells him of his plan to destroy mankind with a flood, Enoch desperately tries to change his mind. Then the Lord shows him the lives they're leading and what they're doing and Enoch changes to the point he's outraged and tells the Lord he should cleanse the earth of them. What the account was trying to get across was that if we knew everything the Lord did, we might understand why he does the things he does.
The scriptures go beyond what's written in the pages. You might try to go to Amazon and buy a few books. In some cases, like King Josiah's reforms, Josiah may have gone too far according to some recent scholars. Margaret Barker, a Methodist scholar, is very thorough and she has some fascinating lectures on YouTube. Two are on a quick trip through the Old Testament and you might find those a good place to start. Then bounce off her lectures and go to others.
When I walk, I listen to lectures instead of music. There's no end to the free stuff you can find on YouTube. I'm not much on evangelical stuff, but try to stat with the scholarly types. You might like trying that.