In a state of flux, what can I do?

This is way complicated, but in a nutshell it's a story of dishonesty, unfaithfulness, topped with more dishonesty and unfaithfulness, compounded by a bunch of difficult dynamics. End the relationship, get healthy and have healthy relationships. Meanwhile hang on to any good family relationships and healthy friendships and concentrate on the new job and finishing the MBA. The person and relationship you described were highly unlikely to have produced the family you want. Get a good counselor and spend some time working out how you got into the situation and learn how to avoid repeating your mistakes. Get yourself prepared for the good marriage and family you hope to eventually have.