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.
On a kinda related note has anyone ever had MT-32 working properly with the limited edition CD version of Judgment Rites? Using the Daum SVN of dosbox (which has munt built into it) I have no trouble with the floppy version but the CD version seems to play a GM track even when setup for MT-32. I have been seeing if anyone on the Vogons website could help as well so if someone is interested in taking a crack at this please also look at http://www.vogons.org/viewtopic.php?f=7&t=35933#p316421