There always will be something related to the divine commandments that our intellect will not be able to completely justify for us. This is where submission is meant to take over from logic. We need to understand that our mere brains cannot grasp the wisdom behind all the commands. We need to grasp that our intellect cannot possibly grasp that which is beyond its reach. Can one expect a three year old to understand the laws of physics?
Similarly, our perception is subjugated to what it’s allowed to perceive, by its Creator. So, if you find yourself challenging a clear order from Allah, or justifying it with invalid reasoning because you fear that you won’t be able to find a tangible reason behind following His commands, then understand that submission should never be dependent on the power of reasoning. If you find yourself questioning your iman or your ‘amal then let your intuition answer it.