Archaicx1: My story will only be partially canon compliant. Final Fantasy 7 is a very linear game, thus, much of what happens in it will happen in my story. At the same time, certain instances are going to end up going differently due to Naruto's presence. I know this probably doesn't answer all of your question, but I don't want to give away any spoilers.
Tellemicus Sundance: Allow me to assuage your fears. Tifa loves Cloud. Period. She will not be getting with Naruto. Neither will Yuffie, for that matter. I may have a one-sided Yuffie/Naruto romance added for comedy purposes. As I said somewhere in the beginning of this story, there is only one possibility for a three-way romance -- which, by the way, do exist in real life -- between Naruto/Aerith/Cissnei, but it's still up in the air on whether I even want to go this route or not. That is something that will likely write itself if, and this is a big IF, it happens.