If you still need a way to extract the .001 files I stumbled upon this util awhile ago http://oezmen.eu/gameresources/
just scroll down the list to Star Trek: 25th Anniversary/Judgment Rites. It worked fine on the floppy version of Judgment rites and mostly fine on the CD version.
I just tried that program, somehow I couldn't get it to work with my neither my Judgment Rites CD nor a floppy version I found on the Internet.
Perhaps, I misunderstood the instructions because I work with DOS programs almost on a daily basis, so that's not the problem.
It would be nice to see how much music I missed / skipped when I captured the MIDI music live from the game.
Also, do you know if there's any music in 25th Anniversary that is not included in Judgment Rites?
And when you ripped music from the 25th Anniversary game, did it sound properly in your MT-32? I know that in Sierra games you have to "record" the MT-32 MIDI music live to get it with the right instrumentation, but I guess that's not the case with the engines used in these games.