With the Pillow fan, are you pulling in air for combustion?...if so, this is actually typical of coal fired boilers where fans pressurised the boiler spaces by a few PSI over atmosphere to aid combustion
So you may need to provide some shim trunking from around the fan 's round cowling, down toward the boiler gas burner area location......
A consequence of not doing this is that the air that the fan draws in will be lost to atmosphere out of the portlights or any air spaces between the deck & the superstructure
The second consequence of no direct air trunking is that the boiler burner will need to draw substantial amounts of free air [oxygen] to maintain combustion....the only way to achieve this is to have a great number of portlights or mesh grill's & doors open
Remember a gas flame with insufficient oxygen will burn with a yellow flame, where as all of your trials without the superstructure fitted yielded a bluish flame at the burner....when you fit a superstructure, you may loose the ability to see the flame
Shim brass of 0.003" thick is an excellent material to use for trunking......it folds well, cut easily with kitchen scissors, and all joints can be soft soldered to make a rigid trunking
[it also returns you to your school days of developing shapes from paper of cardboard
]
Derek