CD3 is mainly command briefing animations (which are not essential) and cutscenes (FS_open compatible theora versions of which are available online). The one file you'd really miss is warble_fs2.vp, which is the game music.
However, I do believe simply running Turey's installer will also download any files you're missing from your retail installation, so you might want to try that before going looking for individual files. I'm not an expert on the installer myself though, as I've never needed it. So that's second hand information. But worth a shot.
Anyway, in case I'm wrong about the installer, I'm attaching a screenshot of what a "normal" FS2 folder should look like, so you can see which files you are missing based on that. Keep in mind that both the freespace2 and the FRED exes will be replaced by their FS_open counterparts anyway (and the open exes have no CD check, by the way), so it doesn't matter if you don't have those. It's the .vp files that really matter.
[Edit] Well, seeing the post above that I missed while posting, it seems the installer will indeed do the trick. So definitely go with that

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