Thanks for your comments.
Boats.net, Intersting suggestion! I think that the smoke exhaust must be located over water level (for that reason the box is full of smoke) and could be the reason why the engines stop when the water level rises, actually I run the boat slowly to reduce the sinking of the engines deep into water after passing waves.
This yamaha enduro 40 hp is the old model that you can still buy in Indonesia (where the boat is located) and for sure is a pre-mix model. New models doesen´t fit in the "box" without making structure modifications, they are very strong, last owner use a pair of them during 8 years without any problems, for that reason I have bought the same ones.
Can I run them with a 1:60 or 1:70 mix Yamalube?, I run them at 75-80% of the maximun power. Will this reduce the smoke?