Hi,
I wouldn't worry too much about the aerodynamics of relatively small windows and a much bigger fuselage. For
starters, Boeing doesn't on the real thing, (well they do but it is way to complicated to do on a model)
and secondly if this is an RC model then if it doesn't fly it isn't the windows that are the problem, it will be something
else. As a general rule, in relative terms most RC models or scale models of any kind are exactly that, a SCALE model.
If you actually scaled up the amount of thrust or speed that the model was ACTUALLY doing it would be a totally
unrealistic number. I recently saw someone calculate a speed of a boat model. The real thing was speed limited to
about 20 knots, if the scaled version was doing the scaled up speed it was actually doing on the water it would have
been thousands of knots. I think you will find the same thing with your model. It might need say 20 Knots to get
airbourne and not stall, if you scale up a 1/25 scale model then 25 x 20 = 500 knots to avoid stalling - I think the FAA
might have something to say about that and there is not a runway on the planet it could take off from.
Cheers
Andrew