Jacob Aagaard has a nice, little section in Excelling at Chess where he discusses a method of preparing an opening.
To start with filter the games in the lines to be studied to only those where the players are rated 2350+. First you will look at the endgames that occur and study those. He recommends printing them out and playing through them on a board. After the endgame he looks at the middlegame. You start by taking the 100-150 highest rated games and play through them. Maintain a list of positional concepts, adding to the list each time you encounter a new positional concept. Then play through 7 or 8 games where a concept occurred. Make a file of your favorite examples for later study and repitition. Finally, look at the actual theory for the opening.
It will take some work, but it sounds like you would have a solid grasp of the opening afterwards.