The only think you may be able to do (why didn't I think about it sooner?) is to record the FM/MIDI songs as digital audio, save them as 11KHz WAV files and replace the existing WAV files of the existing songs with your WAV files. There is a chance it will work as is, if the game does not check file integrity and does not have any specific length restrictions. And if there are problems, in theory you may be able to solve them with binary hacking (e.g., HEX editing) without recompiling the game from the sources you don't have.
Well, I tried this, but I wanted to go further. A few tests showed that in fact, the game has no problems accepting much higher quality .wav files, so since the .wav files in there are a pitiful 11025Hz mono, I decided to embark on a project to replace the music there by the CD audio tracks from the Sega CD version of the game. There was one small problem, namely that the game didn't seem to read more bytes of the replaced file as the size of the original file I replaced, but that was easily solved by just finding and editing those file sizes in the exe, and I ended up spending a day making a tool that could update them automatically.
However, when I actually got to the part where I was figuring out which of the Sega CD tracks corresponded to which of the ~500 .wav files in the game folder, I found out that the SEGA CD was simply missing some tracks. This made me remember a thread on the GOG forum about running MK2 with Gravis Ultrasound, and since this MK1 also supports GUS, I wondered if the GUS midi would be a viable source for filling in those missing tracks. So I set up the game to run with GUS, recorded the intro track with DOSBOX, and compared that with the original .wav from the SFX folder.
Well. Turns out it wasn't just "a viable source". It's simply the source 😵
The recording I made was an exact 44100Hz stereo match of the 11025Hz mono .wav file in the game's files. It turns out that all the .wav files in the sfx folder, besides the actual recorded samples, are simply the output of the Gravis Ultrasound playing the midi music and sound effects of the game.
Furthermore, even in GUS mode, the game still plays the actual recorded samples from the .wav files, making it the ideal solution.
So, conclusion: Use Gravis Ultrasound. It's the best quality audio you can have for the GOG version 😀
The thread about MK2 GUS on gog.com:
https://www.gog.com/forum/mortal_kombat ... ultrasound
And for those who are interested... here's my (now rather useless) tool to update the file sizes in the mk1.exe file:
http://nyerguds.arsaneus-design.com/project_s … hanger/release/
Well. If someone happens to have higher quality versions of the actual recorded samples, or wants to experiment with replacing the .gra files with those from different versions, this could still have some use, I guess 😜