I dont understand what might have gone wrong, all I did to use the program was:
1. extract trekext2.exe and trekext2.pas to the game folder
2. goto the game folder in dosbox
3. type "trekext2 data.dir data.001" or "trekext2 fed.dir fed.001" etc
On the floppy version of STJR it went merrily away and unpacked the .001 file, for the CD it unpacked some then spat an error hence my saying it mostly worked on this version. No issue with ST25th for me either.
Im not sure about any tracks in ST25th that are not in STJR, but I dont think there are any.
Like yourself the only way I personally managed to get MT-32 music out of the game was to use dosbox midi recording. These recordings sounded fine on MT-32. If you want the XMI dumps then I would suggest you follow the link I posted for the STJR patch and ask tikalat how he got them, he is a wiz at driver hacking and has been (along with New Rising Sun) fixing many driver/sound issues for MT-32 and GM in Sierra/Apoggee/Lucasarts/Interplay games.
The port dosbox uses by default for midi is 330. Not sure why it might be hanging as the patch worked perfect for me on my Collectors CD version. Did it black screen before patching with MT-32 selected? Without the patch the game will still run when MT-32 is chosen, it just wont sound quite right.