Two more things that you may be overlooking, if I'm not mistaken you built a conventional boiler and are now comparing it to a good gasser, if you want a real eye opener compare stack temp losses. I would be willing to put money on the table saying that your stack temp will go well over 1000 degrees when it is running hard, the boiler that Honda is running is my old show unit, I used it here to heat about 6800 feet of not great insolation and as hard as we could run it with 8-10 hour burn times we never saw over 450 degrees! A lot of your heat is going up your stack in two forms, 1 heat and 2 unburned fuel ( smoke is unburned fuel )
The second thing that I think we are overlooking is your pump size, early on in our installation business we thought bigger is better, the trouble with that is that if you size the circ to big, it will cavitate and the water will simply not move well, evidence of this happening is when you can audibly hear the circs water over the motor noise, personally I would step down in size to a 0011 or even a 009 with your pipe size and length.
Look at it this way, put a box fan in a room, turn it on, feel the air movement now cover half of the fan with a piece of cardboard, both the velocity and the CFMs will suffer dramatically because of the restriction, the same thing happens with an oversized circ pump, they DO NOT pump, they only circulate!