I don't think you necessarily need a 'system,' just go through each of your minor leagues and every player that has a # next to him, ask yourself if you would care if you lost him? If the answer is no, move on down the list, if the answer is yes, add him to the 40-man if there's space. Once you run out of space, simply prioritize who you would rather keep.
Once complete, make one final spin through the minors, looking for # to ensure you didn't miss anyone.
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