The flame will always be yellow - but not so much so that there is visible smoke. Warped baffles are also common so no clues there......if the burner was unhappy before there will be considerable soot build up in the firebox and baffles. Too much air could make ignition difficult and also makes the flame impinge on the boiler itself - both undesirable! Try opening the air door just a fraction - but make a note of where it originally was. Setting these things up is a balance between pump pressure (150 psi approx), nozzle condition, and air inlet. Ideally we look for 12% CO2 but that isn't any help without a gas analyser!
John, May 2009