I dont know how comprehensively you want to go through all the different aspects of design, but even a shallow pass through this stuff might get quite involved. If there is part of this you dont follow, please dont be afraid to ask questions, and we will try our best to keep on answering.
Yes, the cross-sectional area (and I am going to use the abbreviation X-sectn) of a 5.5 inch diam body is 23.75 sq in, but this is the X-sectn you would use for aerodynamic purposes. For internal loads (the forces, stresses and strains acting inside the structural components), the X-sectn area you are interested in is that of the airframe tube shell, because the empty space inside the shell is not going to support any structural loads.
If you have a body of 5.5 inch diam, the circumference is 17.28 inches (pi times the diam). If we assume a wall thickness of 0.10 inches, the X-sectn area of the airframe tube is 1.73 sq in (circumf times thickness). And if there are any holes or openings in the side walls of the airframe, they represent a weak point because of the structural cutout (loads are slightly concentrated around the edges of the hole) and for the reduced shell X-sectn in that area.
I am guessing that your spreadsheet represents an aerodynamic drag load acting on the front end of your rocket design? Yes, there will be aerodynamic loads, if your rocket ever gets going fast enough. Before that happens, however, you have some significant accelerations and loads that occur during motor burn. You have the thrust force of the motor (most severe during peak thrust) acting against the inertia load of all components of the rocket that are located ahead of the motor mount. The highest levels of internal loads caused by motor thrust will be found in the airframe shell in the zone at, and immediately ahead of, the motor mounts. As you move forward through your rocket design, past the weight of the lower airframe, past the ejection baffles, past the altimeter bay, etc, the weight (actually, mass) of components that are yet further forward is progressively reduced. The upper sections of airframe do not require the structural beef that the lower portions do in order to withstand internal loads due to motor thrust. So if you feel you must reinforce the airframe with fiberglass or carbon fiber, you are wasting your time (and adding lots of dead weight) to add reinforcement to any of the front half (or even two thirds?) of the structure.
Now if you want to build a rocket that will withstand a free-fall from 5,000 feet (ejection failure) and come up out of the ground unscathed, go ahead and reinforce everything. You can even build the front end out of titanium or something.
This ignores the whole matter of the stability (in a structural sense) of the airframe tube, and whether to expect local crippling, column buckling, or other failure modes. Usually something else gets ya long before you approach the raw shear strength limits of the material. Hopefully the manufacturer has performed some realistic tests of his airframe product; you should look for qualifying statements such as 1,000 pound load on a 60-inch-long section or something to that effect. If you want to test this yourself you can perform a simple test in your garage by standing the tube on end (on a cleanly cut, perpendicular end face) and stacking sandbags (of a known weight) on top. The tricky part will be balancing the whole mess, and applying each additional bag GENTLY. Stand clear, dont perform this trick within reach of anything breakable, and dont let the kids play underneath the sandbags. And of course, after you test the tube to failure, it wont be any good to build with.
As far as aerodynamic loads are concerned, an axial load of 1177 pounds acting on 1.73 square inches will give you a stress level of 680 psi. Even if you apply a safety factor of 1.25 to cover the unknown unknowns, the stresses would still only be 850 psi, well within the advertised limit of 1000 psi, without any added airframe reinforcement. If your airframe tube has a wall thickness less than 0.10 inches, you will obviously need to re-run these numbers.
I would bet that some of the experienced HPR guys (sorry, I cant help here because I aint one of em) could give you some rules-of-thumb on which you could base your design. I dont know if the database is really complete enough to try to analyze these designs from an engineering standpoint. It seems you pretty much have to build-n-fly HPR, and adjust the next one to your personal preferences based on experience.
Oh, yeah, almost forgot . . . welcome to TRF!!