Low quality export for stop motion animation stills from Canon 5D Mark ii

Thank you very much beforehand to anyone who is willing to look through this issue, it's been a long and frustrating process so far...
I am attempting to put together a stop motion animation in Final Cut Express but my exports are always either low quality, or medium quality and stretched. I am shooting on a Canon 5D Mark ii set to take pictures at 21M 5616x3744 [999] (though I'm not entirely sure what the 21M or 999 mean).
When I first assembled my stills (unedited or altered in any way) and exported, it looked like this:
A relatively drastic loss in colour and quality. This was achieved exporting through quicktime conversion using the following settings:
Compression Type: H.264
Compressor Quality: Best
Size: 1920x1080 HD
Preserve aspect ratio using: Crop
Deinterlace source video: unchecked
Unhappy with the result, I went through hours of testing and researching which only yielded a result after I discovered the control-Q Easy Setup menu. I tried setting up as an apple intermediate codec using HDV-Apple Intermediate Codec 1080i60 at 29.97 fps. I kept the export settings the same as above, but knowing that I was now working with a canvas that keeps to the 16:9 proportions, I tried cropping one of my stills in photoshop to fit that 16:9 ratio.
I then imported my 16:9 cropped still and an unedited JPEG version from my camera and exported the resulting 10 second video. The result was better quality, but still noticeably degraded from the original stills. More importantly, both the cropped 16:9 and the unedited JPEG were stretched out of proportion as seen below (16:9 version):
Of course I forgot to note the original settings on Easy Setup so I can't figure out how to get back to the original lower quality, yet undistorted image (not that I want to do that). I tried numerous different sizes for the export including changing the Crop (when necessary) setting to letterbox. Nothing worked.
The canvas, however, immediately looked 100% better after switching the Easy Setup to HDV-Apple Intermediate Codec 1080i60 at 29.97 fps. It held the improved quality without distorting the image:
I'm not sure if there's any hope of having a great image quality, but at very least I would like to be able to export at the decent quality of the second screenshot without the stretching and cropping.
I need to have this resolved ASAP for work, I've already wasted too much time here. Any help is so appreciated, I'll be active in providing whatever additional information that I can to responders, though please keep in mind that I'm relatively new to all this, I don't know where to find everything

I've decided just to try to get back to the export that I showed in the first screenshot. That result came before I started tampering with the Easy Setup. Like I said, when I changed the setup the canvas quality improved drastically and the dimensions seemed to fit much better, but the export was vertically stretched and cropped. I just reset my FCE settings and it turns out the default setup is DV-NTSC, but it's giving me a terrible quality still...
I just want to get back to that second screenshot's quality.. Could someone suggest what I should switch the easy setup to for importing stills from my Canon 5D Mark ii to yield the right results?

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Im just starting a new job, and will be creating a handful of films for my new employer.
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What initially inspired me was this music video:
http://www.youtube.com/watch?v=zfcHq0hhFWg
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1) What program does one use to play all the individual pictures taken to create the stop motion animation? In other words, once I have shot all the individual pictures of the objects I want to animate, and am ready to organize them and set a playback speed, what program would I use? Do most people just throw all the pictures into final cut and do it that way?? Or is there a better program?
and
2) How do you cut portions of pictures / drawings / frames out to allow for a deep layering effect? I figure most people take each frame and manipulate it individually using photoshop (cutting portions of an image out so something else can be seen through the void). But is there a better way??
For example, lets say I have two crecent shaped pieces of black paper, and I want them to move towards each other from the left and right sides of the screen, and eventually completely obscure whatever is going on in the background behind the paper images. First I would take a series of pictures, moving the pieces of paper in small increments, until they closed the gap and overlapped each other. From that point, I would lay down whatever video I wanted playing in the background into the timeline. Next, I would import the series of photos with the pieces of paper moving towards each other - then comes the problem. The portion of the pictures used for the animation that is NOT PAPER would be obscuring my background video. So at this point, is it easier to shoot the animation against a white background and just chroma key the white out? Or do most people cut the non paper part out using photoshop? or is there a better way?

frisbee681 wrote:
Hi,
Im just starting a new job, and will be creating a handful of films for my new employer.
I want to create something interesting, and have been leaning towards stop motion animation.
Congratulations on the job. Not many of them out there.
frisbee681 wrote:
1) What program does one use to play all the individual pictures taken to create the stop motion animation? In other words, once I have shot all the individual pictures of the objects I want to animate, and am ready to organize them and set a playback speed, what program would I use? Do most people just throw all the pictures into final cut and do it that way?? Or is there a better program?
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frisbee681 wrote:
2) How do you cut portions of pictures / drawings / frames out to allow for a deep layering effect? I figure most people take each frame and manipulate it individually using photoshop (cutting portions of an image out so something else can be seen through the void). But is there a better way??
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frisbee681 wrote:
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<
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Here's another ask of you Paul.
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Low quality export for stop motion animation stills from Canon 5D Mark ii

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