Are customs stops required for private flights within the Schengen Area? I would like to make a VFR flight from Switzerland to Germany and Germany to France and then France to Switzerland. 

For the first step: Switzerland to Germany I know that I have to fill a custom form AND a flight plan while taking off and landing on an airport with custom services. The same for France to Germany. 

HOWEVER from Germany to France is this rule applicable (note that the plane is registered in Switzerland)? I cannot find an official website?
The European Union has also something called EEA - European Economic Area. Within the EEA it is not required to fill out anything except a flight plan between Germany and France. 
Switzerland, as stated, is not part of the European Economic Area and therefor customs are required. 

Just in addition, Schengen is for passport free travel and not for taxes.