Q: 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