The OP should have concentrated the pic on the burner. That is where the problem is, the reducer and the 90 are installed backward. They probley used the tape to hold it together.
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Also, 3 screws are required in each joint. I don’t see any.
The two things come to mind. Is there enough slope?(apart from the T connection previously mentioned) It would lose hydrostatic pressure given the pipe difference, wouldn’t it? the elevation doesn’t seem to meet the acceptable rise of 1/4" per ft at this angle.
Welcome to the forum, Bill Enjoy!! 
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With both running simultaneously, or even just the boiler running, I would be concerned with backdrafting at the water heater.
You can narrate that, Daniel, as a concern.
And, welcome back to the forum!..Enjoy! 
I did not read all the posts.
The flue from the NG water heater is not secured/fastened or sealed effectively.
Just my 2 cents.
Thanks for that, its a great way to learn