Bismillah

Thank you for your question. For many issues of fate and free will, it is useful to see the circumstances as fate and the choices we make as being of our own volition. That is that we cannot control the time we are born in, the circumstances we are brought up in, the country we live in, and so on, and as such the person we marry will be connected to these circumstances in some way and we cannot control that. On the other hand, the choice of who we marry is our own, even if God has pre-eternal knowledge of that choice, and has put us in the best situation. It is important for us to truly make choices for ourselves as that is what meaningful free will is. 

As for the verses speaking about the humans being created in pairs, this is to do with the human race as a whole (i.e there being males and females) rather than as soul mates. As you are aware Islam allows for polygyny as well as multiple temporary and permanent marriages depending on which marriages work out and for what purpose they are contracted. The concept of soul mates is somewhat alien to the Islamic perspective on marriage as far as I am aware.

May you always be successful