Finally I was able to try it. I did it as explained in the previous post.
The only problem is that in the text files the communication code NEEDS a speech file associated to the dialogue. It got around it by assigning it a non-existing file "nospeech.ogg" (.ogg extension is needed), otherwise the game locks up. I'ts a dirty solution but I can't change the comm code.

For the test I just made the Ur-Quan drone give different messages based on a command line parameter:
  --subs (3do/pc)
so it's possible to choose between the current dialogues based on the speech and the pc version that I'm going to implement. Choosing the pc version does not affect the speech for the dialogues that are shared in both versions: if speech is enabled it will still play. The dialogues added or modified won't have speech but hopefully they shouldn't be many.

moreno@MORENO-2E1399F9 /c/programmi/libs/sdl-1.2.8
$ make native
make install prefix=/usr
make[1]: Entering directory `/c/programmi/libs/sdl-1.2.8'
make[1]: `install' is up to date.
make[1]: Leaving directory `/c/programmi/libs/sdl-1.2.8'

moreno@MORENO-2E1399F9 /c/programmi/libs/sdl-1.2.8
$ export C_INCLUDE_PATH=/c/programmi/libs/SDL-1.2.8/include/SDL:/c/programmi/li
bs/SDL_image-1.2.4/include/:/c/programmi/libs/OpenAL/Include/:/c/programmi/libs
/oggvorbis-win32sdk-1.0/include/:c/programmi/libs/zlib/include/

moreno@MORENO-2E1399F9 /c/programmi/libs/sdl-1.2.8
$ export LIBRARY_PATH=/c/programmi/libs/SDL_image-1.2.4/lib/:/c/programmi/libs/
OpenAL/libs/:/c/programmi/libs/oggvorbis-win32sdk-1.0/lib/:c/programmi/libs/zli
b/lib/

moreno@MORENO-2E1399F9 /d/giochi/sc2/source
$ build.sh uqm config
'echo -n' capable echo found.
Sed stream editor found.
tr found.
Make found.
GNU C compiler found.
windres not found.
Little-endian machine detected.
build/unix/build.sh: sdl-config: command not found
build/unix/build.sh: sdl-config: command not found
Simple DirectMedia Layer not found.

I followed the intstructions in INSTALL.mingw.
I don't know what are the MinGW packages needed so I might miss something.
After unzipping the SDL files I followed the instructions in INSTALL and typed "make native" in MSYS.
What could be wrong? The paths are correct. I followed, I also tried the method of copying the files in mingw directory with the same results.