People will be able to help you better if you can say exactly which files are missing or modified.
Everybody should backup their root partition /dev/mmcblk0p1 before modifying or adding any potentially damaging scripts. Did you back anything up before modifying your kindle?
Some of us can supply missing files to you after you supply us with a list of files that you need. I cannot give you my entire partition backup because it contains amazon intellectual "Property" (whatever that is).... You can get a backup copy of a kindle 3 root partition from "the bay of pirates" it you really need one to repair your kindle.
WARNING: Some of the "how to" methods around here are incomplete and may lead to a bricked kindle, so you REALLY should do a backup before installing them.