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Dave is correct here. Except that it is really "sharpness" and not "focus" we are talking about. 
Your problem is related to aperture size. On wide angle lenses one should "avoid" small apertures in general. Every lens has a "sweet spot" where sharpness is at its best.
Light is "diffracted" around edges of the aperture. This diffraction scatters light at different angles and consequently produces loss of sharpness. This happens on ALL lenses but is especially a problem on wide angle lenses set at small apertures.
Interior shots are usually not a problem to shoot in this aperture range. But outside is where there becomes a possible issue. If the sun will be in the shot the camera is not going to properly meter the scene and may pick an aperture out side the sweet spot.
So the camera meters 1/500,F16. On a clear day with 10:00 to 2:00 sun this setting is not going to work. You can select different metering modes but you should be using "spot". You need to meter specific different parts of the scene to determine the "average" exposure setting. You want to properly expose for MID TONES and the average of the light, dark, and middle parts of the scene should be the average. It is just like setting the black, white and grey point for color correction in photoshop.
A good example of this situation is in a scene with big trees. You want the blue sky but you also want to see the bark texture and colors of the fawna located in the shadow of the tree,
Now we must find a mid tone setting with an aperture in the sweet spot. I normally estimate an exposure setting and adjust by equal stops down until I get the aperture I want. You still have a range but it should be in the sweet spot. Of course adjust up if necessary. Remember that a change in aperture size with equal change in shutter speed will yield the same exposre. Example: F13,1/125 will yield the same exposre as F8,1/1000
Back to the camera setting: 1/125,F13 on the Nikkor ( Fstops are different for different lenses)
Say this is the calculated mid tone setting. Using my method we arrive at 1/1000,F8. Perfect. At least it seems so. Take a test shot, look at the histogram. Humm looks like the sky is blown out. Highlights are all peaked out OR the shadows are under exposed OR both. Well then we have to make a choice. Take a few test shots at different shutter speeds. Pick the histogram that has the best balance. Or decide which to expose for, shadows or highlights. If you bracket your shots and use HDR you should come out with a good pano. If you dont use bracketing then you will still get a good exposure but exposed for only light or dark. Creative Choice here for how you want to photograph the scene.
Your probably thinking why dont I just set the aperture at F/8 and pick a shutter speed that works. Easy enough until you get to moving objects like tree limbs from the wind and especially people or boats floating on the water at a dock. If you wind up with a slow shutter speed then these objects blur on the seams or in general. It is really a problem when bracketing and using HDR. So the trick is to set the highest shutter speed you can get away with but with the largest aperture possible (large apertures = small F numbers).
You can make a little note card table with these values to make it easier to fig out. It also really helps me to take scene notes about the weather conditions/lighting conditions and other exposure issues. Later in post processing I am able to see how I messed up or got it right. As your experience increases your note taking and previous shoots will help you be able to walk into a scene, quickly look around and immediately know what exposure to use. You will just be able to add all this info up in your right quick. It gets easier.
I shoot with a Nikkor 10.5mm so I cannot comment on the Sigma sweet spot. But as Dave said F7 or F8 sounds about right.
Sweet spot on the Nikkor 10.5 is F5.6 to F11 with F8 to F11 being the "bulls eye"
Since your lens has a huge depth of field (basically infinity-- although this can change with distance to the camera especially if you are within 12 inches of an object but you should definitely avoid this situation), you should shoot at infinity focus and rely on the lens depth of field to bring things into focus.
You should be able to shoot 4 without a top and bottom with the Sigma lens. You will have a small pinhole or slightly larger at the top and bottom to patch but that is very easy to do. Convert to a cube, open photoshop and clone out the top hole. Cover the bottom with a tripod cap or patch this one to. Convert back to sphere and do the color correcting in this format to avoid white "cube lines".
Should you shoot a top and bottom then there a few things to consider.
Auto focus should be avoided. The meter of the lens will focus on the closest object and if there is a light fixture hanging from the ceiling it will focus on that and bring you out of infinty focus. This will cause the edges fo the image to be blurry. You may also find that the cameras will not shoot at all in autofocus because it can't locate a focus point. So make sure you are in manual focus set at infinity.
Same thing applies for the bottom shot. Except that if in auto focus the camera will focus on the tripod head and the same thing will occur as above. Again, use manual focus at infinity.
Of course you must shoot at the same settings for ALL images. If you change aperture or shutter speed for the top or bottom there will be color imbalance and the stitched image, although properly stitched, will have a round ring of color imbalance on the floor and ceiling.
General Lee
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Panoweaver
Topic: top bottom shooting tips
