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I'm not aware of a real step-by-step guide, sorry. But netbeans should work fine. However, in order to really use the CDC/PBP platform (which is what is used in the Kindle), you might be better off with Windows (sorry to have to say so), since the Java ME SDK, which brings full platform support for CDC/PBP, is unfortunally only available for Windows. Then you should be able to use the Java ME features of Netbeans.
But I never went that way: I started with just using the J2SE profile, introducing Kindlet.jar and the few other Kindle specific libs. Did you ever try to open e.g. the Sudoku project with netbeans? It should be very much prepared, except for the Kindle .jars which you might have to copy to a proper place and reference them in the project (for the Sudoku project, they in fact _are_ referenced, but you'll probably have them in a different place in the filesystem).
However, now I went a bit further and downloaded Sun's PBP reference implementation 1.1, which is available with their J2ME downloads. It was a bit awkward to have netbeans use them, though. I had to create another J2SE profile, find the XML file netbeans stores the profile's configuration in and edit the boot classpath in there to make it point to the PBP classes.
If you're not quite custom with the Java platform nomenclature, I can't do much more than suggesting to read it all up. It's awkward, sales-people-compromised stuff, but the Java platform has become a small universe you'll have to explore to really understand what part of it you're actually using.
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