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Yup, figured it out.
In the "PPF Patch Engine" page, download the first zip under the yellow subheading "PPF-O-MATIC." Make sure original CDI image, PPF patch, file_id are in the same directory. (More might be needed, but I know these need to be here at least.) Type the command line that you were given in the Sonic 2 fix. You'll see that the program makes no distinction between CDI and CDRwin files.
I'm sure there's a better way, but I just looked at this stuff 5 minutes ago.
Also, if I'm wrong in these steps, SOMEONE PLEASE SAY SO. I'd hate to lead someone down the wrong path, not to mention confusing myself.
--Collin M.--
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