Finally, the tricky user config file was the key to solve most issues...
With the right parameters SNES games work now @full speed with sound@48000Hz ! (@805-850MHz)
With stock frequencies, sound@48000Hz is ok with a bit more audio buffer (4096) and/or frameskip=2.
Now i'll try to 'repair' the GUI if i find time in the next couple of weeks.
Then, making a debian package should be trivial