Excellent story.
And personally, I think you've struck just the right balance between Salazar and Harry. It is to be expected that Harry will no longer be the inexperienced, confused, more than slightly naive boy he is portrayed as in canon now that he has all the memories and skills of his existence as Salazar. And the fact that he was Salazar for an entire, and rather long, lifetime, and was only Harry for fifteen years, makes it only proper that he lean more towards the wordly, slightly jaded crusader aspect of Salazar. And since the core personalities are both extremely similiar in regards to qualities, beliefs, and perceptions, it makes the current balance seem very much like a Harry Potter that is much older, wiser, and more experienced than a Salazar Slytherin who has taken over Harry Potter's body.
Anyway, great story.