I guess there is always a first time, but normally water heaters are so basic they are boring to repair. When I was diagnosing, I always broke the system into parts. Since you have an overflame condition, it suggests a misalignment or an overpressure possibility. As I said earlier, the manufacturers all design their components to fail to the low pressure side and in 30 years I never one time saw an over pressure condition from the regulator, but I guess anything could be possible.
I would start with manometer at the cooktop to verify pressure from the regulator at the tanks. You start there because it is super easy to hook a manometer to one of the burner spigots. If pressure there is correct, 10-14″ water column, it should be good through the whole system in that there is no way for it to be too high anywhere if it is not too high there.
Next, check for the correct orifice. This is not a common issue, however one thing that always amazed me was how often folks thought the problem was not enough gas so they drilled out the orifice. There should be a number stamped on the orifice and you can find the correct orifice number online. They are cheap and easy to swap in a new one.
If the pressure is good and the orifice is good, it is a burner issue and I can’t tell you more about sorting that one out as has to be a mechanical issue i.e. alignment, etc.. If you were close, I would say just bring it by the house. Diagnosing at a distance is hard, hands on is usually much simpler.
As you likely discovered the service manual for this water heater is online and is the same one I used for years http://waterheatertimer.org/pdf/Atwood-Water-Heater-Service-manual.pdf
Steve and Andra
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