Wow - that's a tough one. I think there are probably many different ways of addressing what you've mentioned, so I'll give you a few of my own personal thoughts with the caveat that what works for one writer may not work for another...
Getting the material 'out of your brain to construct it and get a good story out of it': If I had to take a wild guess I would say that the most likely problem here is that you're starting your screenplay before you've got your story worked out. I've written 12 feature-length screenplays in the past 15 years and I've tried many different methods - all of which had their merits.
I still play around some with my approach depending on the specifics of the project I'm working on, but now, more often than not, I know what every single scene from start to finish will be, and I have it outlined on paper, before I ever start the actual first draft of the script. That's not to say that things won't change as the actual screenplay begins to unfold, but without this outlining/planning process I found I was much too prone to finding out something didn't quite work or was too vague and muddled after already writing half of my movie.
So it sounds to me like you're starting the actual script before you've finished developing your story. Can you tell someone your story/movie from start to finish? I find this can be immensely helpful as well - describe your movie to someone verbally and you will very quickly find what parts don't work or haven't been fully thought out. Then comes the hard part: going back to the 'drawing board'.
I've found the planning stages, before actual pages of the screenplay itself are being written to be the most crucial part of the process for me - this is where my story is developed and tested and then, once I feel that I've got a great, exciting compelling story, I begin the first draft.
It can be tough to resist the urge to jump right in, but I think you'll find that forcing yourself to put in the extra work up front will pay off in the long run and save you both time and headaches.
One more thing - I've found that there's no 'magical' process in writing that can take the place of plain ol' hard work. Nothing beats putting your arse in that chair every single day to write - whether you feel like it or not. Or as Edison put it, "Genius is one percent inspiration and ninety-nine percent perspiration."
My $0.02...
Luke