I just, well, didn't.
Rather than picking words from my Harry Potter readings at random, I could do it in a much more focused, precise way because CL can inform me of which words are the most frequently used words.
And if they're frequently used, obviously I can find them in Harry Potter.
So now I just downloaded some guy's list of the top 2k most common words in Czech. I'm going to go through it and mark the ones which I definitely do know. The ones I do not know I am going to search for in a PDF of Harry Potter (post chapter 11, where I am), and highlight them for when I come across them later.
If I were more hardcore, I could probably somehow investigate the list and verify its authenticity but I am going to assume that any of the first 2k words made by almost anybody using almost any method are probably going to be pretty good, and the words I pick can't become less based on random factors (though, to be honest - I am not a complete moron! I pick words which I truly have no idea what they could mean from the context - and sometimes after I pick 'em, I figure it out. So yeah, it's not entirely random what I pick. I also try to get a variety of POS)
I seriously can't believe I didn't think of doing this earlier. It would have been much more logical.