I asked this question to Rabbi Mordechai Kornfeld, the rosh kollel of iyun hadaf in harnof http://dafyomi.co.il

he replied: "There is a difference of opinion among the Torah authorities as to whether this section should be studied by the typical student of the Torah. Many Torah luminaries maintain that one should not seek philosophical proofs of G-d's existence. Belief in Hash-m should be based on the Mesorah (tradition) that we received from our elders and mentors, the study of Hash-m's wondrous Torah, and the many ways He manifests Himself in His creations and in our daily lives."



UPDATE:

(after more study of the shaar yichud)

ray: The reason the shaar yichud is so difficult is because the author tries to explain logically why we exist. ultimately this involves trying to understand that which is Eternal, and the Eternal is beyond the grasp of human logic, since it is beyond our cause/effect way of understanding things. the shaar yichud itself concludes that it is better to stay away from logical inquiry and to try to know God through His deeds as written in [ch.10][1]:

> Therefore, you should exert your mind until you know the Creator
> through the evidences of His works and not strive to know Him in His
> glorious essence. For He is exceedingly close to you from the side of
> His deeds but infinitely remote in any representation of His essence
> or comparison with it. As already stated, we will never be able to
> find Him in this way. When you arrive at the stage where you abandon
> (trying to find Him) through your thoughts and senses because He
> cannot be grasped in this way, and you instead find Him in the
> evidence of His deeds, as though He were inseparable from you - this
> is the pinnacle of knowledge of Him which the prophet exhorts us on.


  [1]: http://dafyomireview.com/article.php?docid=398#ch10