Alright, I think I can help here. Not help you make it, I'm doing my own anime film
But at least I can teach you what I've learned in this process. The first thing you need to figure out with this story is what archetype it fits. From what you've described, it seems there are martial arts involved, and you want a love interest to develop between your main character and the girl next door. The next thing you need to decide is "how does this ultimately end." Do the guy and girl get together and fight together? Do they dominate the school? What happens after that? Do they end up being world martial arts champs? Or do they end up fighting monsters? I believe that every good story needs a definite end. And I think for your first production, you should consider a short but powerful story. With that said, let's look at the steps you should carefully consider.
CHARACTERS: You really like your characters, right? You want other people to like them too, right? Then the best way to do this is to write emotion driven characters, and have them respond to situations realistically. It's also a very good idea to have them change over the course of your story. One dimensional (as in they don't change at all) characters are good for things like villans and sidekicks and comic relief, but I think you'll find that in the best stories, those kinds of characters change as well. Now, what do I mean about emotion driven characters? Well, you want to SHOW your audience what happens to your character and how the character responds to that situation. Never TELL them, SHOW them. So in each situation they are in, think carefully about what kind of person they are and how they'd respond. Try not to break character, unless something calls for it, such as the character has a life-changing revelation and decides to change to reflect that.
STRUCTURE: Good stories have structure. I'm sure you have some good ideas, but you might not know where in the structure they should fit, or how to use them the best way. Very basically there are 3 parts. Introduction, Body, and Conclusion. There are sub-parts, and I use an 8 step process to write my stuff, but these are the very basics which you can use to figure out where you're going.
INTRODUCTION: Who are the characters? What do they do? What are they normally like? What world do they live in?
BODY: Something happens. What is it? How do the characters react? What do they decide to do? There should be some sort of conflict here, something out of the norm of the daily life of the character. Something that makes them stop and have to deal with the situation. This section is where the beef of your story happens, this is where relationships are made and characters start to change.
CONCLUSION: Everything comes to a conclusion. In your case, do the guy and girl get together? Do they defeat their enemies? Do they change for the better? For the worse?
Alright. That's story stuff. Just tidbits to consider.
Now, the bigger problem...how to make it. All I can really tell you here is how I am doing it, and why I decided to do what it is that I'm doing. I went to college for animation, having not much of an art background (I always drew stuff but I was terrible) and halfway through school realized that I would rather tell my own stories than work on somebody else's ideas. Not only did I decide this, but I decided I would learn everything it takes to do all of it that I can myself. I think the tipping point, the thing that made me realize that it was indeed possible, was watching Shinkai's "Voices of a Distant Star." This is not the kind of thing you can just decide to do and then sit around and not do. You gotta be willing to put all your free time into it. I realized early on that I could not count on other artists/animators/people to help with the project and see it the same way I did, unless I paid them for their services. Which you say you've done? Contracted?
Anyway, I spent most of graduate school trying to learn all the stuff I would need to do this myself. I spent 6.5 years in college and got 3 degrees. Do I regret it? Hell no. I'd do it all over again if I could, only this time I'd focus on actually MAKING the thing as I was learning how to do it. Do you have to spend all that time and money to learn? I'm not sayin you need to go out and go to college and do all that stuff, but if you want to see it succeed, then yes, you'll need to spend a hell of a lot of time to learn how to do things. Or, have a lot of money to pay people to do things you can't. So my advice is start small. Start like, AMV small. Make a trailer for your production, or a 5 minute animation. This is advice that I myself did not take, so do what you will.
I decided the quickest and most streamlined way for me to create something was in 3D. It plays to my strengths as I am not a great 2D artist. I can get by if I have to, but there's no way I could do a movie in 2D. On the other hand, I can model, texture, rig, animate, etc. in 3D. So I just have to spend the time getting my models looking really sharp, and it will be possible. Cel shading has come a long way. Anyway, that's enough of a post for now, I'll check again later and see if there's more I need to share :p If you ever just want to ask questions/talk about production, feel free to pm me.
Also, the link in my sig is to my blog for my movie "Akazawa."