That's really, really strange - emdebian repo is meant to be used together with official repositories, and on my Kindle it worked perfectly (before upgrade to 5.3.0 :P). If you really want to get rid of some of the repos, then remove emdebian and leave official one enabled.
I used emdebian only because of PWs 2GB storage and my 512MB Debian partition, to reduce used amount of space. If you have more available space, you don't really need it.
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