Ok I'm going through compiling my own code now, perhaps these instructions will get me there

Well this just gets better and better.
- Compiled the source
- Moved fs2_open_r to gamedir
- chmod a+x fs2_open_r
- ./fs2_open_r
It runs, plays FSPort cutscene, although this may have something to do with lasting running this game data with FSPort mod from Windows.
Anyway, sound seems fine in the menus, I try to enter briefing room, and it dumps me to desktop with the following output. Now I'm in a 1366x768 desktop with a 640x480 viewport and I need to scroll around the desktop.
$ ./fs2_open_r -spec -glow -mipmap -jpgtga -orbradar -mod Media_VP
bt_audio_service_open: connect() failed: Connection refused (111)
bt_audio_service_open: connect() failed: Connection refused (111)
bt_audio_service_open: connect() failed: Connection refused (111)
bt_audio_service_open: connect() failed: Connection refused (111)
AL lib: alsa.c:675: set access failed: Invalid argument
Segmentation fault
I then thought I'd try altering the .fs2_open/fs2_open.ini but it didn't exist. So I ran fs2_open again then quit it just to see if the crash prevented the ini from being created. But this time I got the output:
$ ./fs2_open_r -spec -glow -mipmap -jpgtga -orbradar -mod Media_VP
Unrecognized command line parameter "-jpgtga". Ignoring...
bt_audio_service_open: connect() failed: Connection refused (111)
bt_audio_service_open: connect() failed: Connection refused (111)
bt_audio_service_open: connect() failed: Connection refused (111)
bt_audio_service_open: connect() failed: Connection refused (111)
AL lib: alsa.c:675: set access failed: Invalid argument
Not entirely sure if the game quit or crashed since I was trying to quit. Either way, I still don't have an INI file to edit to up the resolution.
I've noticed that I'm running 3.6.13, which I wasn't expecting, not sure if that changes things?
Ok, found fs2_open.ini, changed to 1024x768 and now the game launches and plays fine.
Anyway, thought I'd try another different set of instructions for building YAL, so I tried:
$ qmake-qt4 yal.pro
$ make
make -f Makefile.Release
make[1]: Entering directory `/media/storage/Wine_D/Freespace 2/trunk'
/usr/bin/uic-qt4 ui/MainWindow.ui -o ui_MainWindow.h
make[1]: /usr/bin/uic-qt4: Command not found
make[1]: *** [ui_MainWindow.h] Error 127
make[1]: Leaving directory `/media/storage/Wine_D/Freespace 2/trunk'
make: *** [release] Error 2
dan@acer-ubuntu:/media/storage/Wine_D/Freespace 2
Obviously that failed miserably, not sure how to proceed with YAL.
Additionally in game, a couple missions have coughed up some real evil sound distortion.
In the middle of the 'Stop Asteroids from hitting Bastion' mission, the white noise very quickly faded it and became so loud i had to take off my headphones.
I paused the game with Esc, and the noise disappeared and I had perfect sound again. It did this about 15-20 times in that mission, until the last time I did it, the white noise stopped and then all sound just went dead.
So I finished the mission, quit the game, and I was left with a black screen with a white mouse, couldn't figure out how the hell the get back to desktop. I went to console with Ctrl Alt F1 and tried to kill fs2_open_r process, which I did, but that didn't seem to change matters on my Desktop. So I run 'reboot'.
Back in the game, when I was playing the 'Escort Plato to the Jump Node' mission, the sound problem happened only once, but didn't return.
Ok, got YAL to compile and it now runs and runs FSO fine, I had to run:
sudo apt-get install libxtst-dev build-essential libqt4-dev qt4-qmake