Beau,
I am trying to form a mental image of the burner you are describing. The burners on the #14, #12, and #40 are all rectangular and sit horizontally abouve the floor of the firebox a couple of inches. The larger opening is the oil passage. Beneath the oil passage is a long, narrow slit running the width of the burner. Steam is blown through the slit. Oil flows through the large opening and drops down on the steam spray without ever touching the floor of the firebox (if your oil is burning on the floor, you do not have enough atomizer going--and burning oil ends up running onto the ground!). On the above-referenced locomotives and using recycled motor oil that is warmed somewhat by a tank heater and then a line heater, it takes 4-6" of steam pressure on the atomizer to maintain a spot fire, and 15-20" of steam pressure to atomize the oil when working the locomotives. There is a mix of fast hand work with various knobs and levers and a little black magic to keep an oil fire going without either creating "burning of Rome" smoke or loosing your fire up the stack. Oil fires are noisy; stationary, there is the constant hiss of the atomizer, and when running the firebox rumbles and thumps. BTW, while there is a large draft opening in the firebox floor or just above the floor in a side sheet, there is also a modest opening surrounding the burner itself, which allows the draft of the working locomotive to help kick up and swirl the oil. It is a messy and less-than-clean combustion process, which is why you get at least some visible smoke even from the cleanest stack and why you have to periodically sand the firebox and flues to scrub out the carbon deposits formed by the fire. It's amazing how a thin film of carbon coating everything will reduce your firing capacity; the soot is a pretty good insulator, apparently. All the oil-burning locomotives at the museum burn an appalling number of barrels of oil each day, and most of the available latent heat in the oil just goes up the stack (which is why we have diesel-electric locomotives).
I would echo what J.B. Bane says about the refractory brick, which goes from real hot when standing to a bright, glowing orange color when working. The brick continues to pour heat into the boiler even after turning down the fire when making a station stop, and you need to have the gun (injector) going as you stop to avoid losing a lot of steam out the pops.
My image of your grandfather's burner tell me that he does not have the oil flowing directly onto the atomizer as both enter the firebox and that you probably have insufficient atomizer pressure. Sounds to me like a burner redesign would be an appropriate step to take.
Mike