Don't know why the 744 would be at a lower AoA, haven't noticed that. Are you sure it is? The longer and different fuselage shape could just be making it appear to be different. Winglets are unlikely to be making that much difference, but some other issue, such as flap config could.
The B-52 cruising nose low would not be due to any CG position particularly, but rather due to being lighter as opposed to heavier. Aircraft are not attached like a pendulum to anything, so the location of the weight doesn't affect them the same way that it would if they were attached to a tether.
Jet, you posted that "The angle of Incidence...the chord line relative to the longitudinal axis.....is designed so that under all instances of balance the jet cruises nose up and that the stabiliser always exerts a positive downward force. "
Perhaps read it again. While what you wrote is true taken as separate issues, there is not a relation per se. To say that the angle of incidence will affect the body angle in flight is true. It is true that the angle of incidence is designed so that the "under all instances of balance the jet cruises nose up" and it is also true that the "stabilizer always exerts a positive downward force". However, it would not be accurate that the angle of incidence is set to the others are necessarily true. There are many factors involved, including what the optimum mach cruise speed is, the altitude range for cruise flight, etc.
There are many factors here. I took issue with how you tied these factors together, an apparent confusion of causation with association.