I was thinking last night after I posted, that my estimate of what scores could be on disc 2 was based on the idea of the scores being in series order. Your post mentions production order. Neither one of those is necessarily the obvious choice.
Returning to Jeff Bond's indispensable book, the scoring schedule is on page 33. Why wouldn't that be the obvious order for the CDs?
That schedule on p. 33 is actually the reference I used to cite the episode order in my last post. That listed scoring order we've both cited for early season 2 is identical to production order for those episodes that featured original scores.
Bond lists 34 episodes with original music. We've learned during the runup to this release that that number may not be 100% accurate – there is at least some new music in Way To Eden, for example – but it's pretty close. 34 episodes over 15 discs gives a little over two scores per disc. But not all of them were full scores; some were full and some were just part scores. I think Kaplan's score for Enemy Within was a full score, so I'd guess it would take up half a CD. But Steiner's scores for Corbomite, Balance of Terror, and Little Girls were all part scores – in fact they were all recorded the same day. Those three probably combine to take up another half CD.
And we don't know how much additional material there might be, and whether things like unused, alternate, or diegetic cues would be on the same discs as their associated episodes (as was the case with Batman: TAS
Volume 2, e.g.) or on additional discs at the end (as was the case with the Ron Jones set).