My mother did Istikhara for my marriage and it came out positive. However, they broke it off after visiting the boy's house. And now I have done an Istikhara and my heart is inclined towards marrying him. What should I do?
Istikhara in the Shi'i tradition answers the question of "what should I do?", not "what will happen?" It is useful if you have a clear choice in front of you ("should/shouldn't I do this?") and the ability to act on that choice.
From your question, it sounds like you currently do not have the choice to marry or not-marry him. That is, the matter is not in your hands. Therefore, if the question was just, "Should I marry him?", that is not a valid question.
However, if the question was something like "should I encourage my mother to reconsider the marriage?" and the answer was yes, I doubt there is any harm in doing that.
(I don't get the sense that he is asking you to marry him without your family's permission and you are trying to decide whether or not to do it. If that is your situation, feel free to submit another question.)