Frank,
This info is posted under an Aqua Hot thread and this info is for an Aqua Hot. On another post I saw Hydro Hot and little of this info would probably apply, so first thing is to sort out which heating unit type and which thread applies.....
For Aqua Hot:
Changing the nozzle is the first thing to do as well as clean the electrodes and set the gap. If the filter bowl has any debris or has not been recently changed then this would be a good time to do that also. Usually there is a metal gauge tool screwed onto the side of the burner. If you do not have one, buy one. Look at some photos/service manual as to where it gets placed to be sure you are gauging properly. The round plate behind the nozzle is supposed to be lose and float free, it moves to seal the air flow at the nozzle area, check for that. Danfoss nozzles are providing a better track record for being problem free according to Roger Berke who repairs these units and also runs a forum about these heaters, so I would buy that brand.
While in there remove the burner chamber insert and examine it to see if any deformities or melting has occurred and replace it if necessary. Brush and clean the carbon out of the chamber and exhaust area. When this all goes back together you need to be sure this all seals properly and no wires get pinched while mounting the burner. The banjo bolts should be snug but not over tightened.
At this point if the new nozzle, the fuel pump, bearings, and motor are all working properly you should have a clean burning exhaust with literally no smoke after the first minute or two of warm up. The nozzle flow/pattern, the motor speed, the fuel pump pressure, and proper air sealing of the burner assembly sets the air fuel ratio which in one form or another is your problem.
If the new nozzle does not fix your burner smoking issue then motor bearings (slowing down due to drag) and fuel pump pressure (needs a nozzle pressure gauge fixture) is what you probably need to check next. Orman or Roger would be good sources for wisdom and parts. These units will carbon back up quickly if they are not burning cleanly so you can waste effort cleaning what is not fixed.....Hope this helps.
Later Ed