This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
I agree with Rusty. Java is the wrong tool for this job. Partly because such low-level work varies so much between different hardware. Java is a high-level language that is meant to be platform-indepenedent. Even if you could find a way to make Java work at such a low-level, it would lose that. Instead, you should use Assembly or C which are both much better tools for this type of work.