1. How are we to understand the Bible story according to its stated texts it seems at times so contradicting to the values that Judaism seems to claim to express?
2. Why is it written in such a manner where it needs so much explanation and interpretation?
3. How do the principles of a God not missing anything, being all perfect, still have a desire for mankind? If he created man to bestow on him the ultimate pleasure of the divine connection why did he create shame those necessitating us to earn that pleasure to get to fully appreciate it?
4. Is trying to learn, understand our purpose, questioning God‘s ways and intentions, something that is encouraged according to the Torah or is it the ideal to just believe with blind faith in the tradition without trying to comprehend via a rational manner why to stick to all the laws, rituals, customs, etc of the religion that were born into?
Each of these complex questions deserves a lengthy answer beyond the short scope of this framework. Nevertheless, I’ll try to be concise as well as helpful.
1. Regarding mitzvot or passages in the Torah that seem to contradict the Torah’s values and morality, see the previous answer at the following link:
In addition, one has to really analyze each and every issue in unto itself (see also the next point). For example, many ask about Akeidat Yitzchak without realizing that the climax in the story is not (!) to sacrifice your son. Until then, child-sacrifice was considered a religious virtue, until God says here: “Don’t even touch the child”. “No more child-sacrifices!” From then on, the more religious you are, the more moral you’re expected to be.”
2. The Torah is ingeniously written to include many different commentaries which harmonize together to give a much broader picture and understanding (as l’havdil, poets often do). It’s not meant to be read, but to be studied in depth. From personal experience, the more you analyze, the more you appreciate and love the Torah.
3. God, by definition, is perfect, and doesn’t need or “gain” anything from this world. Nevertheless, He created the world out of altruism (=selfless giving, to give to us without gaining, which is part of His perfection), to give us the ultimate perfect gift, which is the soul (=a spark of Himself) in “His image”, giving us the possibility to emulate or copy Him (for our sake). The Torah is the guidelines to teach us how to realize our Godly potential (according to the 13 Godly traits and ideals, see Shmot/Exodus 34, 6-7). In general, the challenges of life are to strive to choose well and to destine our fate as individuals, nations, mankind, and universe. Thus, we “earn” our goodness, and are the much more independent (=like God), and don’t eat from the “bread of shame” like a begger.
4. Rav Kook teaches that in our generation, we have matured and are ready to do the mitzvot, not out of fear or peer pressure, but out of true identification with God and His ideals. Not to just observe the do’s and don’ts “because He said so” or because our parents or society said so, but out of internalization, love and genuine identification, which are deepened by questioning, analysis and study of the Torah and God's Ways. As we return to Israel and approach the redemption, God wants the deep and beautiful Torah to be re-discovered, loved and chosen with self-motivation and free-will.