Stefan, I think you should first complete the equivalent of the sample chapter, which is ~250 kanji. Those are the easiest and can be learned in under a week. This will give you the basics of how the method works. Don't skip this.

Then, if you want to use the flashcards on Reviewing the Kanji, don't use the Greasemonkey script. You need the selection of kanji from somewhere in this thread. Then whenever you learn 10-20 at a time, you paste them into the Manage > Add Custom Selection page. Then Review the blue pile (new cards).

The website doesn't have a builtin support for custom sequences yet, so you'd want to keep your RTK Lite text file that you can continue to copy the kanji from. I think this is the list you can use.

Now as for the technique itself, you want to do the first 250 kanji or so to understand how primitives work. Then you do the kanji in the RTK Lite sequence. Whenever you see a primitive you didn't learn yet, just flip backward through the (book) pages, and learn the primitives (the ones with a * instead of a frame number).