You need to go full manual everything. Put the camera into Manual Mode and pick an aperture that will get the desired Depth of Field. Scan the scene, watching the needle. Whenever the needle moves to the right move the shutter speed down until the needle is in the middle. When you find the brightest part of the scene take a picture and check the LCD. If it doesn't look right adjust the shutter speed. Make sure it's bright enough without blowing anything out. You have to make a judgement call here as to whether or not that is the right exposure...
When you have it right use that picture as the image to be used for a Custom White Balance. (Check your manual on this, as I don't know your camera.)
Now you will have everything locked in - shutter, aperture, and white balance. So you won't get the banding that you see in your picture.
Now take your shots and be sure to overlap each shot, from 25% to 33% on each. This gives the stitching program a way to compare two pics to see how they should line up.
You should get a very good pano this way.
Now if you want to turn that into an excellent pano, other programs can do a lot. Canon's software can do a very good job, Autostich a bit better, but the best panos (in my opinion) use PanoTools. PanoTools is extremely difficult to use so several people have written front ends. PTAssembler is the best but the most difficult to use ($30 I think). PTGui is much easier but has limitations that you might not notice until you get very good at it. It's a little pricey at $60. Hugin is much like PTGui, opensource and free, but possibly not a full product yet. It's current version is MORE than enough to do the job, and did I mention is was free?
The three above can also use "helper" programs, all free. Autosift, Enblend, and Smartblend can all help with certain points in the process, like matching for seams and blending the seams.
Check out the Quick Tour from PTGui to get an idea of what can be done: http://www.ptgui.com/examples/quicktour5/
Max Lyons, author of PTAssembler, stitched 196 frames to create a 1 gigapixel image: http://www.tawbaware.com/maxlyons/gigapixel.htm
He has some awesome shots on his pages.
Here's a shot I did with PTGui, 68 megapixels: http://photography-on-the.net/forum/showthread.php?t=102740