[Edit: I've just seen that you already have this one sorted. However, in case anyone else needs it, here is the post I wrote in reponse to the nav lights and rotating beacon...]
Page 10 of the manual is wrong re: the nav lights (I have sent JF a support ticket about this). They are controlled by the rheostat switch on the left of the lighting panel (page 21 of the manual).
When the nav lights are switched on, the rotating beacon comes on, too. (Thank you to @RetiredMan93231 for telling me about that one - unfortunately, the manual doesn't mention the rotating beacon at all.)
The anti-collision rocker switch controls only the strobe.