Killing myself over a stop motion project...

So I'm trying to figure out how best to edit a few jpeg sequences (around 2,00 pictures total) into a high quality movie. I've plugged the image sequence into quicktime pro 7, transcoded it to Pro Res 422, and edited in Final Cut 7, but the quality of the images has decreased dramatically.

I've read on this forum that After Effects is the way to go when trying to create a stop motion movie w/ jpegs. I've tried multiple times, but keep getting frames of color bars, odd dimensions. etc. I'm clearly a novice at this stuff!

I would ideally like to edit in FCP, as that is what I'm most comfortable with, but am open to ANY suggestions.

Thanks,