Still not much 'autonomy' but I do finally have everything in place. The Raspberry pi, the Arduino, a 433 MHz radio and the remote control receiver, all neatly packed in the waterproof box at the back.
The Scanning Sonar is mounted as well, so I can finally map the lake.
A bit to my surprise it showed a nearly flat bottom, at 80 cm. Then I realized that this sonar works at 1 MHz, and it probably just shows the top of the fluid mud layer. I will need a lower frequency (like 200 kHz) to get to the 'real' bottom.