how fix yamaha 40 running rough ?

Hi
it sounds like your engine could have lost ignition to one cylinder, start the engine up on flush muffs or in a test tank and kee[ing your self dry, use a pair of insulated pliers(rubber coated handle) to pull off one spark plug cap at a time and replace it after a few seconds.
if the engine stops when you pull one cap of then the engine was running on that cylinder ok.
if there is no difference to the engine running then that plug is doing nothing productive so change that spark plug for a new one, if that doesnt work go to the HT coil on that cylinder and test it, work back along that circuit until you find the fault.

Greasy
September 2010