read this article.
http://www.deanoshiro.com/brakes/brakearticle.html
Its been posted here before Im sure. If youre asking these kind of questions and working on a 1000hp car I really hope you read as much as you can before you proceed as you are working on the most important safety feature on the car. And most important, get professional help. Not as far as installation, im sure youre fine with that, I mean more with design.
If you've got 1000hp, I'm sure you're not going to be working with vacuum assist power brakes, so that leaves you with Hydra-boost or manual. I recommend manual.
Check out the CL ad for dual tandem brake master setup with a balance bar thats a bolt on mod. There is a local guy that makes them. If youre interested Ill dig up his number.
Also, Drilled rotors are only good for one thing. Cracking into pieces to be scattered onto the pavement as you hit the nearest tree.